gromacs →
2021.3-2 →
armhf → 2021-09-07 21:59:20
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| gromacs 2021.3-2 (armhf) Tue, 07 Sep 2021 15:33:16 +0000 |
+==============================================================================+
Package: gromacs
Version: 2021.3-2
Source Version: 2021.3-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-e9222f5d-d145-466a-8538-1c6f348fe53b' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/gromacs-6PKBLz/resolver-czXLx3' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.7 MB in 14s (1796 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gromacs' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/debichem-team/gromacs.git
Please use:
git clone https://salsa.debian.org/debichem-team/gromacs.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 86.5 MB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main gromacs 2021.3-2 (dsc) [3083 B]
Get:2 http://172.17.0.1/private bookworm-staging/main gromacs 2021.3-2 (tar) [48.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main gromacs 2021.3-2 (tar) [38.0 MB]
Get:4 http://172.17.0.1/private bookworm-staging/main gromacs 2021.3-2 (diff) [40.9 kB]
Fetched 86.5 MB in 18s (4926 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gromacs-6PKBLz/gromacs-2021.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gromacs-6PKBLz' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: chrpath, cmake (>= 3.13), debhelper-compat (= 13), gcc-11, g++-11, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libx11-dev, lsb-release, mpi-default-bin, mpi-default-dev, zlib1g-dev, build-essential, fakeroot
Filtered Build-Depends: chrpath, cmake (>= 3.13), debhelper-compat (= 13), gcc-11, g++-11, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libx11-dev, lsb-release, mpi-default-bin, mpi-default-dev, zlib1g-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [486 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [542 B]
Fetched 1985 B in 0s (42.1 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev binutils
binutils-arm-linux-gnueabihf binutils-common bsdextrautils chrpath cmake
cmake-data cpp-11 debhelper dh-autoreconf dh-strip-nondeterminism
distro-info-data dwz file g++-11 gcc-11 gcc-11-base gettext gettext-base
gfortran-10 groff-base ibverbs-providers intltool-debian libarchive-zip-perl
libarchive13 libasan6 libatomic1 libbinutils libblas-dev libblas3
libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcbor0 libcc1-0
libctf-nobfd0 libctf0 libcurl4 libdebhelper-perl libedit2 libelf1
libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7
libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1
libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libgcc-11-dev libgcc-s1 libgfortran-10-dev
libgfortran5 libgomp1 libhwloc-dev libhwloc-plugins libhwloc15
libibverbs-dev libibverbs1 libicu67 libjs-jquery libjs-jquery-ui
libjsoncpp24 liblapack-dev liblapack3 libltdl-dev libltdl7 libmagic-mgc
libmagic1 libmd0 libmpdec3 libncurses6 libncursesw6 libnghttp2-14
libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev
libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev
libpmix2 libprocps8 libpsl5 libpthread-stubs0-dev libpython3-stdlib
libpython3.9-minimal libpython3.9-stdlib librdmacm1 librhash0 librtmp1
libsigsegv2 libssh2-1 libstdc++-11-dev libstdc++6 libsub-override-perl
libtinfo6 libtool libubsan1 libuchardet0 libuv1 libx11-6 libx11-data
libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6
libxext6 libxml2 libxnvctrl0 lsb-release m4 man-db media-types
mpi-default-bin mpi-default-dev ocl-icd-libopencl1 openmpi-bin
openmpi-common openssh-client po-debconf procps python3 python3-minimal
python3.9 python3.9-minimal sensible-utils x11proto-dev xorg-sgml-doctools
xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc binutils-doc cmake-doc
ninja-build gcc-11-locales dh-make gcc-11-doc gettext-doc libasprintf-dev
libgettextpo-dev gfortran-10-doc libcoarrays-dev groff lrzip liblapack-doc
libboost-doc libboost1.74-doc libboost-atomic1.74-dev
libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
libboost-program-options1.74-dev libboost-python1.74-dev
libboost-random1.74-dev libboost-regex1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libfftw3-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils
libstdc++-11-doc gcj-jdk libx11-doc libxcb-doc m4-doc apparmor less
www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh
monkeysphere ssh-askpass libmail-box-perl python3-doc python3-tk
python3-venv python3.9-venv python3.9-doc binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl javascript-common
libgpm2 libcoarrays-openmpi-dev publicsuffix xauth libmail-sendmail-perl
psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils chrpath cmake
cmake-data cpp-11 debhelper dh-autoreconf dh-strip-nondeterminism
distro-info-data dwz file g++-11 gcc-11 gcc-11-base gettext gettext-base
gfortran-10 groff-base ibverbs-providers intltool-debian libarchive-zip-perl
libarchive13 libblas-dev libblas3 libboost-dev libboost1.74-dev libbrotli1
libbsd0 libcbor0 libcurl4 libdebhelper-perl libedit2 libelf1 libevent-2.1-7
libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev
libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libgcc-11-dev libgfortran-10-dev
libgfortran5 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev
libibverbs1 libicu67 libjs-jquery libjs-jquery-ui libjsoncpp24 liblapack-dev
liblapack3 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libmpdec3
libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200
libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3
libpciaccess0 libpipeline1 libpmix-dev libpmix2 libprocps8 libpsl5
libpthread-stubs0-dev libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librdmacm1 librhash0 librtmp1 libsigsegv2 libssh2-1
libstdc++-11-dev libsub-override-perl libtool libuchardet0 libuv1 libx11-6
libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev
libxdmcp6 libxext6 libxml2 libxnvctrl0 lsb-release m4 man-db media-types
mpi-default-bin mpi-default-dev ocl-icd-libopencl1 openmpi-bin
openmpi-common openssh-client po-debconf procps python3 python3-minimal
python3.9 python3.9-minimal sbuild-build-depends-main-dummy sensible-utils
x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
The following packages will be upgraded:
binutils binutils-arm-linux-gnueabihf binutils-common libasan6 libatomic1
libbinutils libcc1-0 libctf-nobfd0 libctf0 libgcc-s1 libgomp1 libncursesw6
libstdc++6 libtinfo6 libubsan1
15 upgraded, 135 newly installed, 0 to remove and 59 not upgraded.
Need to get 213 MB of archives.
After this operation, 850 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [968 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf libtinfo6 armhf 6.2+20201114-4 [328 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libncursesw6 armhf 6.2+20201114-4 [105 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf gcc-11-base armhf 11.2.0-3+rpi1 [205 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf libgcc-s1 armhf 11.2.0-3+rpi1 [36.1 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libstdc++6 armhf 11.2.0-3+rpi1 [466 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.7-2+rpi1 [794 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.2.10-2 [73.4 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.7-2+rpi1 [1631 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.7-2+rpi1 [1618 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf python3.9 armhf 3.9.7-2+rpi1 [480 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-5 [60.5 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-5 [475 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf libmd0 armhf 1.0.3-3 [27.2 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210714-1 [81.0 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libfido2-1 armhf 1.8.0-1 [55.9 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf openssh-client armhf 1:8.4p1-6 [794 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libctf0 armhf 2.37-5+rpi1 [79.5 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libctf-nobfd0 armhf 2.37-5+rpi1 [138 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf binutils-arm-linux-gnueabihf armhf 2.37-5+rpi1 [2165 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libbinutils armhf 2.37-5+rpi1 [411 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf binutils armhf 2.37-5+rpi1 [62.2 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf binutils-common armhf 2.37-5+rpi1 [2286 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf cmake-data all 3.18.4-2+rpi1 [1725 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [580 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.9.0-3 [151 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf libcurl4 armhf 7.74.0-1.3 [305 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf libjsoncpp24 armhf 1.9.4-4 [67.0 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf librhash0 armhf 1.4.2-1 [141 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf libuv1 armhf 1.40.0-2 [119 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf cmake armhf 3.18.4-2+rpi1 [3118 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf cpp-11 armhf 11.2.0-3+rpi1 [42.1 MB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.1 [192 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf libcc1-0 armhf 11.2.0-3+rpi1 [37.8 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf libgomp1 armhf 11.2.0-3+rpi1 [88.1 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf libatomic1 armhf 11.2.0-3+rpi1 [8176 B]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf libasan6 armhf 11.2.0-3+rpi1 [2045 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf libubsan1 armhf 11.2.0-3+rpi1 [795 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf libgcc-11-dev armhf 11.2.0-3+rpi1 [699 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf gcc-11 armhf 11.2.0-3+rpi1 [48.1 MB]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:79 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:80 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:81 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:82 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:83 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.1 [1056 kB]
Get:84 http://172.17.0.1/private bookworm-staging/main armhf distro-info-data all 0.51 [7508 B]
Get:85 http://172.17.0.1/private bookworm-staging/main armhf libstdc++-11-dev armhf 11.2.0-3+rpi1 [1952 kB]
Get:86 http://172.17.0.1/private bookworm-staging/main armhf g++-11 armhf 11.2.0-3+rpi1 [45.8 MB]
Get:87 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-3+rpi1 [234 kB]
Get:88 http://172.17.0.1/private bookworm-staging/main armhf libgfortran-10-dev armhf 10.2.1-6+rpi1 [278 kB]
Get:89 http://172.17.0.1/private bookworm-staging/main armhf gfortran-10 armhf 10.2.1-6+rpi1 [7195 kB]
Get:90 http://172.17.0.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:91 http://172.17.0.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:92 http://172.17.0.1/private bookworm-staging/main armhf libibverbs1 armhf 33.2-1 [52.4 kB]
Get:93 http://172.17.0.1/private bookworm-staging/main armhf ibverbs-providers armhf 33.2-1 [25.0 kB]
Get:94 http://172.17.0.1/private bookworm-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:95 http://172.17.0.1/private bookworm-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:96 http://172.17.0.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-9 [9534 kB]
Get:97 http://172.17.0.1/private bookworm-staging/main armhf libboost-dev armhf 1.74.0.3+b1 [4820 B]
Get:98 http://172.17.0.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [167 kB]
Get:99 http://172.17.0.1/private bookworm-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [126 kB]
Get:100 http://172.17.0.1/private bookworm-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [100 kB]
Get:101 http://172.17.0.1/private bookworm-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB]
Get:102 http://172.17.0.1/private bookworm-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-1 [61.7 kB]
Get:103 http://172.17.0.1/private bookworm-staging/main armhf libevent-dev armhf 2.1.12-stable-1 [281 kB]
Get:104 http://172.17.0.1/private bookworm-staging/main armhf librdmacm1 armhf 33.2-1 [60.0 kB]
Get:105 http://172.17.0.1/private bookworm-staging/main armhf libfabric1 armhf 1.11.0-2 [311 kB]
Get:106 http://172.17.0.1/private bookworm-staging/main armhf libfftw3-double3 armhf 3.3.8-2 [429 kB]
Get:107 http://172.17.0.1/private bookworm-staging/main armhf libfftw3-single3 armhf 3.3.8-2 [633 kB]
Get:108 http://172.17.0.1/private bookworm-staging/main armhf libfftw3-bin armhf 3.3.8-2 [43.6 kB]
Get:109 http://172.17.0.1/private bookworm-staging/main armhf libfftw3-dev armhf 3.3.8-2 [1060 kB]
Get:110 http://172.17.0.1/private bookworm-staging/main armhf libhwloc15 armhf 2.4.1+dfsg-1 [122 kB]
Get:111 http://172.17.0.1/private bookworm-staging/main armhf libnuma1 armhf 2.0.12-1 [22.5 kB]
Get:112 http://172.17.0.1/private bookworm-staging/main armhf libnuma-dev armhf 2.0.12-1 [35.6 kB]
Get:113 http://172.17.0.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.6-15 [388 kB]
Get:114 http://172.17.0.1/private bookworm-staging/main armhf libltdl-dev armhf 2.4.6-15 [159 kB]
Get:115 http://172.17.0.1/private bookworm-staging/main armhf libhwloc-dev armhf 2.4.1+dfsg-1 [190 kB]
Get:116 http://172.17.0.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.16-1 [51.0 kB]
Get:117 http://172.17.0.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:118 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:119 http://172.17.0.1/private bookworm-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:120 http://172.17.0.1/private bookworm-staging/main armhf libx11-data all 2:1.7.2-1 [311 kB]
Get:121 http://172.17.0.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.7.2-1 [705 kB]
Get:122 http://172.17.0.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.3-1.1 [47.8 kB]
Get:123 http://172.17.0.1/private bookworm-staging/main armhf libxnvctrl0 armhf 470.57.02-2 [26.0 kB]
Get:124 http://172.17.0.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.2.14-2 [39.9 kB]
Get:125 http://172.17.0.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.4.1+dfsg-1 [19.9 kB]
Get:126 http://172.17.0.1/private bookworm-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:127 http://172.17.0.1/private bookworm-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:128 http://172.17.0.1/private bookworm-staging/main armhf libibverbs-dev armhf 33.2-1 [179 kB]
Get:129 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB]
Get:130 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB]
Get:131 http://172.17.0.1/private bookworm-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:132 http://172.17.0.1/private bookworm-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:133 http://172.17.0.1/private bookworm-staging/main armhf libpmix2 armhf 4.1.0-3 [470 kB]
Get:134 http://172.17.0.1/private bookworm-staging/main armhf libopenmpi3 armhf 4.1.0-10+rpi1 [1768 kB]
Get:135 http://172.17.0.1/private bookworm-staging/main armhf openmpi-common all 4.1.0-10+rpi1 [177 kB]
Get:136 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:137 http://172.17.0.1/private bookworm-staging/main armhf libpmix-dev armhf 4.1.0-3 [629 kB]
Get:138 http://172.17.0.1/private bookworm-staging/main armhf openmpi-bin armhf 4.1.0-10+rpi1 [205 kB]
Get:139 http://172.17.0.1/private bookworm-staging/main armhf libopenmpi-dev armhf 4.1.0-10+rpi1 [1143 kB]
Get:140 http://172.17.0.1/private bookworm-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:141 http://172.17.0.1/private bookworm-staging/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:142 http://172.17.0.1/private bookworm-staging/main armhf x11proto-dev all 2020.1-1 [594 kB]
Get:143 http://172.17.0.1/private bookworm-staging/main armhf libxau-dev armhf 1:1.0.9-1 [22.3 kB]
Get:144 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:145 http://172.17.0.1/private bookworm-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:146 http://172.17.0.1/private bookworm-staging/main armhf libxcb1-dev armhf 1.14-3 [171 kB]
Get:147 http://172.17.0.1/private bookworm-staging/main armhf libx11-dev armhf 2:1.7.2-1 [779 kB]
Get:148 http://172.17.0.1/private bookworm-staging/main armhf lsb-release all 11.1.0+rpi1 [28.1 kB]
Get:149 http://172.17.0.1/private bookworm-staging/main armhf mpi-default-bin armhf 1.14 [4752 B]
Get:150 http://172.17.0.1/private bookworm-staging/main armhf mpi-default-dev armhf 1.14 [5548 B]
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Setting up gfortran-10 (10.2.1-6+rpi1) ...
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Setting up libfabric1 (1.11.0-2) ...
Setting up libpmix2:armhf (4.1.0-3) ...
Setting up libopenmpi3:armhf (4.1.0-10+rpi1) ...
Setting up libpmix-dev:armhf (4.1.0-3) ...
Setting up openmpi-bin (4.1.0-10+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up mpi-default-bin (1.14) ...
Setting up libopenmpi-dev:armhf (4.1.0-10+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up mpi-default-dev (1.14) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-13+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.2.1-6+rpi1 g++-11_11.2.0-3+rpi1 gcc-10_10.2.1-6+rpi1 gcc-11_11.2.0-3+rpi1 libc6-dev_2.31-13+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++-11-dev_11.2.0-3+rpi1 libstdc++6_11.2.0-3+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.2.4 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11.1+rpi1 base-passwd_3.5.51 bash_5.1-2 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.36.1-8 build-essential_12.9 bzip2_1.0.8-4 chrpath_0.16-2 cmake_3.18.4-2+rpi1 cmake-data_3.18.4-2+rpi1 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 cpp-11_11.2.0-3+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.77 debhelper_13.5.1 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 distro-info-data_0.51 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.2-2 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 g++-11_11.2.0-3+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-11_11.2.0-3+rpi1 gcc-11-base_11.2.0-3+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.3.0-22+rpi1 gettext_0.21-4 gettext-base_0.21-4 gfortran-10_10.2.1-6+rpi1 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hostname_3.23 ibverbs-providers_33.2-1 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libapt-pkg6.0_2.2.4 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan6_11.2.0-3+rpi1 libassuan0_2.5.3-7.1 libatomic1_11.2.0-3+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.37-5+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36.1-8 libboost-dev_1.74.0.3+b1 libboost1.74-dev_1.74.0-9 libbrotli1_1.0.9-2+b1 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-13+rpi1 libc-dev-bin_2.31-13+rpi1 libc6_2.31-13+rpi1 libc6-dev_2.31-13+rpi1 libcap-ng0_0.7.9-2.2+b1 libcbor0_0.5.0+dfsg-2 libcc1-0_11.2.0-3+rpi1 libcom-err2_1.46.2-2 libcrypt-dev_1:4.4.18-4 libcrypt1_1:4.4.18-4 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcurl4_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.1 libdpkg-perl_1.20.9+rpi1 libedit2_3.1-20210714-1 libelf1_0.185-2 libevent-2.1-7_2.1.12-stable-1 libevent-core-2.1-7_2.1.12-stable-1 libevent-dev_2.1.12-stable-1 libevent-extra-2.1-7_2.1.12-stable-1 libevent-openssl-2.1-7_2.1.12-stable-1 libevent-pthreads-2.1-7_2.1.12-stable-1 libexpat1_2.2.10-2 libext2fs2_1.46.2-2 libfabric1_1.11.0-2 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfftw3-bin_3.3.8-2 libfftw3-dev_3.3.8-2 libfftw3-double3_3.3.8-2 libfftw3-single3_3.3.8-2 libfido2-1_1.8.0-1 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-11-dev_11.2.0-3+rpi1 libgcc-s1_11.2.0-3+rpi1 libgcrypt20_1.8.7-6 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran-10-dev_10.2.1-6+rpi1 libgfortran5_11.2.0-3+rpi1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-5 libgomp1_11.2.0-3+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-6 libhogweed6_3.7.3-1 libhwloc-dev_2.4.1+dfsg-1 libhwloc-plugins_2.4.1+dfsg-1 libhwloc15_2.4.1+dfsg-1 libibverbs-dev_33.2-1 libibverbs1_33.2-1 libicu67_67.1-7 libidn2-0_2.3.0-5 libisl23_0.23-1 libjs-jquery_3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui_1.12.1+dfsg-8 libjsoncpp24_1.9.4-4 libk5crypto3_1.18.3-6 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-6 libkrb5support0_1.18.3-6 libksba8_1.5.0-3 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.57+dfsg-3 liblocale-gettext-perl_1.07-4+b1 libltdl-dev_2.4.6-15 libltdl7_2.4.6-15 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.3-3 libmount1_2.36.1-8 libmpc3_1.2.0-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnuma-dev_2.0.12-1 libnuma1_2.0.12-1 libopenmpi-dev_4.1.0-10+rpi1 libopenmpi3_4.1.0-10+rpi1 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-9 libpam-modules-bin_1.4.0-9 libpam-runtime_1.4.0-9 libpam0g_1.4.0-9 libpciaccess0_0.16-1 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-4+deb11u1 libpipeline1_1.5.3-1 libpmix-dev_4.1.0-3 libpmix2_4.1.0-3 libprocps8_2:3.3.17-5 libpsl5_0.21.0-1.2 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.7-2+rpi1 libpython3.9-stdlib_3.9.7-2+rpi1 librdmacm1_33.2-1 libreadline8_8.1-1 librhash0_1.4.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-8 libsqlite3-0_3.34.1-3 libss2_1.46.2-2 libssh2-1_1.9.0-3 libssl1.1_1.1.1k-1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++-11-dev_11.2.0-3+rpi1 libstdc++6_11.2.0-3+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.3-6+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_11.2.0-3+rpi1 libuchardet0_0.0.7-1 libudev1_247.3-6+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-8 libuv1_1.40.0-2 libx11-6_2:1.7.2-1 libx11-data_2:1.7.2-1 libx11-dev_2:1.7.2-1 libxau-dev_1:1.0.9-1 libxau6_1:1.0.9-1 libxcb1_1.14-3 libxcb1-dev_1.14-3 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1.1 libxml2_2.9.10+dfsg-6.7 libxnvctrl0_470.57.02-2 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.2-2 lsb-base_11.1.0+rpi1 lsb-release_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.36.1-8 mpi-default-bin_1.14 mpi-default-dev_1.14 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 ocl-icd-libopencl1_2.2.14-2 openmpi-bin_4.1.0-10+rpi1 openmpi-common_4.1.0-10+rpi1 openssh-client_1:8.4p1-6 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-4+deb11u1 perl-base_5.32.1-4+deb11u1 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 procps_2:3.3.17-5 python3_3.9.2-3 python3-minimal_3.9.2-3 python3.9_3.9.7-2+rpi1 python3.9-minimal_3.9.7-2+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.17 sysvinit-utils_2.96-7 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.36.1-8 x11proto-dev_2020.1-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: gromacs
Binary: gromacs, gromacs-data, libgromacs6, libgromacs-dev, libnblib0, libnblib-dev, gromacs-mpi
Architecture: any all
Version: 2021.3-2
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Nicholas Breen <nbreen@debian.org>
Homepage: https://www.gromacs.org/
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/debichem-team/gromacs
Vcs-Git: https://salsa.debian.org/debichem-team/gromacs.git
Testsuite: autopkgtest
Testsuite-Triggers: build-essential, perl
Build-Depends: chrpath, cmake (>= 3.13), debhelper-compat (= 13), gcc-11 [!mipsel !mips64el] | gcc-9 [mipsel mips64el], g++-11 [!mipsel !mips64el] | g++-9 [mipsel mips64el], libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libx11-dev, lsb-release, mpi-default-bin, mpi-default-dev, zlib1g-dev
Build-Depends-Indep: doxygen, ghostscript, graphicsmagick, graphviz, mscgen, python3-sphinx, rdfind, symlinks, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra
Package-List:
gromacs deb science optional arch=any
gromacs-data deb science optional arch=all
gromacs-mpi deb science optional arch=any
libgromacs-dev deb libdevel optional arch=any
libgromacs6 deb libs optional arch=any
libnblib-dev deb libdevel optional arch=any
libnblib0 deb libs optional arch=any
Checksums-Sha1:
3d04316553b1fba1ec4812e9c0368cb00235924d 48515038 gromacs_2021.3.orig-regressiontests.tar.gz
645f186b8d4b999be78b8b0726f1908251ca43f4 37987972 gromacs_2021.3.orig.tar.gz
0a09438b0a97fb36fec736a3398de316508e6637 40864 gromacs_2021.3-2.debian.tar.xz
Checksums-Sha256:
dc90616e4f20055cb56315d936bbb1be1c9c8a9645b77a85419361933c2d43f1 48515038 gromacs_2021.3.orig-regressiontests.tar.gz
e109856ec444768dfbde41f3059e3123abdb8fe56ca33b1a83f31ed4575a1cc6 37987972 gromacs_2021.3.orig.tar.gz
7d9ebf8b27d9227e104026d9041389590765ede95dc14d2305bc77ccca6f8db3 40864 gromacs_2021.3-2.debian.tar.xz
Files:
93956ea42c4d16fdd541518c05972989 48515038 gromacs_2021.3.orig-regressiontests.tar.gz
1850870fbbfb228051ee0afc1c5ddeff 37987972 gromacs_2021.3.orig.tar.gz
d616586f03896bd003d8f0c979f40983 40864 gromacs_2021.3-2.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.Mc8800yn/trustedkeys.kbx': General error
gpgv: Signature made Fri Aug 20 20:33:39 2021 UTC
gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F
gpgv: issuer "nbreen@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gromacs_2021.3-2.dsc
dpkg-source: info: extracting gromacs in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gromacs_2021.3.orig.tar.gz
dpkg-source: info: unpacking gromacs_2021.3.orig-regressiontests.tar.gz
dpkg-source: info: unpacking gromacs_2021.3-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying readme.patch
dpkg-source: info: applying copyright-file.patch
dpkg-source: info: applying disable-cpuinfotest.patch
dpkg-source: info: applying mdrun-test-timeout.patch
dpkg-source: info: applying local-mathjax.patch
dpkg-source: info: applying mpi-tests-localhost.patch
dpkg-source: info: applying i386-disable-specific-tests.patch
dpkg-source: info: applying hppa-disable-ewaldunittest.patch
dpkg-source: info: applying manual-image-conversion.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=e040c44591bf400793155c77e2e04554
JOURNAL_STREAM=8:7708138
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-e9222f5d-d145-466a-8538-1c6f348fe53b
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c92440
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package gromacs
dpkg-buildpackage: info: source version 2021.3-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh_testdir
dh_testroot
rm -rf build docs/doxygen/*.pyc
dh_clean build-basic build-mpi build-manual configure-stamp
debian/rules binary-arch
dh_testdir
(mkdir -p build/basic; cd build/basic; CC=/usr/bin/gcc-11 CXX=/usr/bin/g++-11 cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2021.3-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DGMX_INSTALL_LEGACY_API=ON )
-- The C compiler identification is GNU 11.2.0
-- The CXX compiler identification is GNU 11.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc-11 - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++-11 - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.6") found components: Interpreter
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 3 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 0
-- Detected build CPU stepping - 3
-- Detected build CPU features - neon
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic
(mkdir -p build/basic-dp; cd build/basic-dp; CC=/usr/bin/gcc-11 CXX=/usr/bin/g++-11 cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2021.3-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DGMX_DOUBLE=ON)
-- The C compiler identification is GNU 11.2.0
-- The CXX compiler identification is GNU 11.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc-11 - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++-11 - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.6") found components: Interpreter
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Using default binary suffix: "_d"
-- Using default library suffix: "_d"
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 3 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 0
-- Detected build CPU stepping - 3
-- Detected build CPU features - neon
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic-dp
(mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2021.3-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi" -DGMX_LIBS_SUFFIX="_mpi")
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.6") found components: Interpreter
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Using manually set binary suffix: "_mpi"
-- Using manually set library suffix: "_mpi"
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 3 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 0
-- Detected build CPU stepping - 3
-- Detected build CPU features - neon
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- The mdrun-only build is deprecated
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpi
(mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2021.3-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d" -DGMX_LIBS_SUFFIX="_mpi_d")
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /usr/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.6") found components: Interpreter
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Using manually set binary suffix: "_mpi_d"
-- Using manually set library suffix: "_mpi_d"
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 3 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 0
-- Detected build CPU stepping - 3
-- Detected build CPU features - neon
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
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[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/simulatoralgorithm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp:77:
/<<PKGBUILDDIR>>/build/basic/src/buildinfo.h:75: warning: "HWLOC_VERSION" redefined
75 | #define HWLOC_VERSION "2.4.0"
|
In file included from /usr/include/hwloc.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp:64:
/usr/include/arm-linux-gnueabihf/hwloc/autogen/config.h:15: note: this is the location of the previous definition
15 | #define HWLOC_VERSION "2.4.1"
|
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/11/bits/stl_vector.h: In function ‘_ZN11PairlistSet18constructPairlistsERKN5Nbnxm7GridSetEN3gmx8ArrayRefI14PairsearchWorkEEP16nbnxn_atomdata_tRKNS4_11ListOfListsIiEEiP6t_nrnbP19SearchCycleCounting._omp_fn.0’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void PairlistSet::constructPairlists(const Nbnxm::GridSet&, gmx::ArrayRef<PairsearchWork>, nbnxn_atomdata_t*, const gmx::ListOfLists<int>&, int, t_nrnb*, SearchCycleCounting*)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/energyhistory.cpp:43:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function ‘std::enable_if_t<gmx::IsSerializableType<T>::value, void> gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<T>) const [with T = double]’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:442:1: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
442 | ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<T> values) const
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/interaction_const.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/multipletimestepping.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:63:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function ‘std::enable_if_t<gmx::IsSerializableType<T>::value, void> gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<T>) const [with T = double]’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:442:1: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
442 | ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<T> values) const
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void init_gtc_state(t_state*, int, int, int)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor ‘gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)’:
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor ‘gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)’:
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:368:1: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
368 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function ‘real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)’:
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function ‘real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)’:
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function ‘void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)’:
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function ‘std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)’:
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<pull_coord_work_t>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<pull_group_work_t>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<pull_group_work_t>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type ‘std::vector<pull_group_work_t>::iterator’ changed in GCC 7.1
2297 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type ‘std::vector<pull_group_work_t>::iterator’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type ‘std::vector<pull_group_work_t>::iterator’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type ‘std::vector<pull_group_work_t>::iterator’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void allocStatePrevStepPullCom(t_state*, const pull_t*)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_mapping>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘void prune_ss_legend(t_matrix*)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_gyrate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_h2order.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hbond.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helixorient.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hydorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_lie.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saltbr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sans.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saxs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sham.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sigeps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sorient.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spatial.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tcaf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function ‘void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1329:13: note: parameter passing for argument of type ‘gmx::ArrayRef<t_mapping>’ changed in GCC 7.1
1329 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function ‘void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:250:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
250 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function ‘void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1034:31: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
1034 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1035 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1034:31: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
317 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:318:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
318 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:318:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function ‘int gmx_xpm2ps(int, char**)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1377:20: note: parameter passing for argument of type ‘gmx::ArrayRef<t_mapping>’ changed in GCC 7.1
1377 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1377:20: note: parameter passing for argument of type ‘gmx::ArrayRef<t_mapping>’ changed in GCC 7.1
1377 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genion.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp
In file included from /usr/include/c++/11/string:40,
from /usr/include/c++/11/bits/locale_classes.h:40,
from /usr/include/c++/11/bits/ios_base.h:41,
from /usr/include/c++/11/streambuf:41,
from /usr/include/c++/11/bits/streambuf_iterator.h:35,
from /usr/include/c++/11/iterator:66,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:54,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:41:
In static member function ‘static constexpr std::size_t std::char_traits<char>::length(const char_type*)’,
inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::assign(const _CharT*) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/11/bits/basic_string.h:1458:19,
inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(const _CharT*) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/11/bits/basic_string.h:689:28,
inlined from ‘void read_ab(char*, const char*, MoleculePatch*)’ at /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:115:25:
/usr/include/c++/11/bits/char_traits.h:371:32: warning: ‘unsigned int __builtin_strlen(const char*)’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
371 | return __builtin_strlen(__s);
| ~~~~~~~~~~~~~~~~^~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp: In function ‘void read_ab(char*, const char*, MoleculePatch*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:88:10: note: at offset 48 into source object ‘a’ of size 48
88 | char a[4][12];
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function ‘void process_pull_groups(gmx::ArrayRef<t_pull_group>, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const t_blocka*, char**)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:453:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘gmx::index’ {aka ‘int’} [-Wformat=]
453 | "Number of weights (%ld) for pull group %d '%s' does not match the number of "
| ~~^
| |
| long int
| %d
454 | "atoms (%ld)",
455 | gmx::ssize(pullGroup.weight), g, pullGroupNames[g].c_str(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| gmx::index {aka int}
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:454:33: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 8 has type ‘gmx::index’ {aka ‘int’} [-Wformat=]
454 | "atoms (%ld)",
| ~~^
| |
| long int
| %d
455 | gmx::ssize(pullGroup.weight), g, pullGroupNames[g].c_str(),
456 | gmx::ssize(pullGroup.ind));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| gmx::index {aka int}
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {float}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::AnalysisDataValue>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {float&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::AnalysisDataValue>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::AnalysisDataDisplacementModule::frameFinished(const gmx::AnalysisDataFrameHeader&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::AnalysisDataValue>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::AnalysisDataValue>::iterator’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function ‘void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef<const gmx::AnalysisDataValue>)’:
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:584:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::AnalysisDataValue>’ changed in GCC 7.1
584 | void AnalysisDataStorageFrameData::addPointSet(int dataSetIndex,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function ‘void gmx::AnalysisDataStorageFrame::finishPointSet()’:
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:715:27: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::AnalysisDataValue>’ changed in GCC 7.1
715 | data_->addPointSet(currentDataSet_, firstColumn,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
716 | makeConstArrayRef(values_).subArray(begin, end - begin));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:715:27: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::AnalysisDataValue>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/coordinatefile.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/outputselector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setforces.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setprecision.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energydrifttracker.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In member function ‘void ForeignLambdaTerms::finalizePotentialContributions(gmx::ArrayRef<const double>, gmx::ArrayRef<const float>, const t_lambda&)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:173:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
173 | void ForeignLambdaTerms::finalizePotentialContributions(gmx::ArrayRef<const double> dvdlLinear,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function ‘void accumulatePotentialEnergies(gmx_enerdata_t*, gmx::ArrayRef<const float>, const t_lambda*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:235:65: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
235 | enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda, *fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/freeenergyparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gpuforcereduction_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function ‘void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<float> >, history_t*, gmx::ForceBuffersView*, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, gmx::ArrayRef<const float>, t_forcerec*, gmx::MdrunScheduleWorkload*, gmx::VirtualSitesHandler*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:645:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
645 | enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
646 | *inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
651 | enerd->term[F_COM_PULL] += awh->applyBiasForcesAndUpdateBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
652 | inputrec->pbcType, mdatoms->massT, foreignLambdaDeltaH, foreignLambdaDhDl, box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
653 | forceWithVirial, t, step, wcycle, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp: In member function ‘void gmx::UpdateConstrainGpu::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp:73:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_grp_tcstat>’ changed in GCC 7.1
73 | void UpdateConstrainGpu::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp: In member function ‘void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:396:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
396 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:396:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:418:45: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
418 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
419 | forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:418:45: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationgrid.h:105:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
105 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp: In member function ‘gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
105 | gmx::ArrayRef<const double> Bias::calcForceAndUpdateBias(const awh_dvec coordValue,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
146 | convolvedBias = state_.updateProbabilityWeightsAndConvolvedBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
147 | dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | &probWeightNeighbor);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
152 | updateForceCorrelationGrid(probWeightNeighbor, neighborLambdaDhdl, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:154:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
154 | state_.sampleCoordAndPmf(dimParams_, grid_, probWeightNeighbor, convolvedBias);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:154:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
168 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
170 | tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
180 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
181 | dimParams_, grid_, coordState.umbrellaGridpoint(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
182 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{}, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
192 | state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
193 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
146 | convolvedBias = state_.updateProbabilityWeightsAndConvolvedBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
147 | dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | &probWeightNeighbor);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp: In member function ‘real gmx::Awh::applyBiasForcesAndUpdateBias(PbcType, const real*, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, const real (*)[3], gmx::ForceWithVirial*, double, int64_t, gmx_wallcycle*, FILE*)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:294:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
294 | real Awh::applyBiasForcesAndUpdateBias(PbcType pbcType,
| ^~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:294:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:350:85: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
350 | gmx::ArrayRef<const double> biasForce = biasCts.bias_.calcForceAndUpdateBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
351 | coordValue, neighborLambdaEnergies, neighborLambdaDhdl, &biasPotential,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
352 | &biasPotentialJump, commRecord_, multiSimRecord_, t, step, seed_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:350:85: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:350:85: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.h:70,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:48:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BiasCoupledToSystem>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In constructor ‘gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*, int, int)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biassharing.cpp
In file included from /usr/include/c++/11/memory:63,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp:47:
/usr/include/c++/11/bits/stl_algobase.h: In function ‘_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >; _Predicate = __gnu_cxx::__ops::_Iter_pred<gmx::BiasGrid::hasLambdaAxis() const::<lambda(const auto:22&)> >]’:
/usr/include/c++/11/bits/stl_algobase.h:2061:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
2061 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~
/usr/include/c++/11/bits/stl_algobase.h:2061:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp
/usr/include/c++/11/bits/stl_algobase.h: In function ‘bool gmx::pointsAlongLambdaAxis(const gmx::BiasGrid&, int, int)’:
/usr/include/c++/11/bits/stl_algobase.h:2114:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
2114 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2115 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algobase.h: In function ‘bool gmx::pointsHaveDifferentLambda(const gmx::BiasGrid&, int, int)’:
/usr/include/c++/11/bits/stl_algobase.h:2114:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
2114 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2115 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/dimparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:61,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::GridAxis>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, int, const int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::GridAxis>::iterator’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biaswriter.cpp
/usr/include/c++/11/bits/vector.tcc: In constructor ‘gmx::BiasGrid::BiasGrid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, int, int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::GridAxis>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::BiasGrid&, const string&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In function ‘void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:351:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::PointState>’ changed in GCC 7.1
351 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, int, gmx::ArrayRef<const double>, gmx::ArrayRef<double>) const’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:475:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
475 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:475:8: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
508 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:529:38: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
529 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, neighborLambdaDhdl, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:529:38: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
539 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:549:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
549 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
550 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:549:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:553:69: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
553 | double newPotential = calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
554 | dimParams, grid, coordState_.umbrellaGridpoint(), neighborLambdaDhdl, newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:553:69: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘void gmx::BiasState::sampleProbabilityWeights(const gmx::BiasGrid&, gmx::ArrayRef<const double>)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1350:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1350 | void BiasState::sampleProbabilityWeights(const BiasGrid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘void gmx::BiasState::sampleCoordAndPmf(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, double)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1404:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1404 | void BiasState::sampleCoordAndPmf(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp: In member function ‘void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::BiasGrid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp:129:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const BiasGrid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationhistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘double gmx::BiasState::updateProbabilityWeightsAndConvolvedBias(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >*) const’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1242:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1242 | double BiasState::updateProbabilityWeightsAndConvolvedBias(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp: In member function ‘void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::CorrelationBlockData>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In constructor ‘gmx::CorrelationTensor::CorrelationTensor(int, int, double)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
1159 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/read_params.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function ‘double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
78 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function ‘double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
210 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:243:56: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
243 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:243:56: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<pme_setup_t>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<float> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/device_management.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/membedholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function ‘void gmx::LegacySimulator::do_md()’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1289:34: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_grp_tcstat>’ changed in GCC 7.1
1289 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1290 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1291 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1292 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationinput.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationinputhandle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulatorbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long int, std::allocator<long long int> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In static member function ‘static void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx_file_position_t>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function ‘t_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:116:11: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
116 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_rgb>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_rgb>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘gmx::index search_col(t_psdata*, real, real, real)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.6.0.0 ../../lib/libgromacs.so.6 ../../lib/libgromacs.so
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cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/forcecalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp
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cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/gmxcalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/gmxsetup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/integrator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/integrator.cpp
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cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/interactions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/molecules.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/particlesequencer.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/particletype.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/particletype.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/simulationstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/topologyhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/topology.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/transformations.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=0 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/setup.cpp
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/usr/bin/g++-11 -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib.so.0 -o ../../lib/libnblib.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/forcecalculator.cpp.o CMakeFiles/nblib.dir/gmxcalculator.cpp.o CMakeFiles/nblib.dir/gmxsetup.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o ../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib.so.0.1.0 ../../lib/libnblib.so.0 ../../lib/libnblib.so
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++17 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
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[ 0%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 0%] Built target scanner
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/gcc-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 3%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp: In member function ‘void gmx::ComputeGlobalsElement<algorithm>::compute(gmx::Step, unsigned int, gmx::SimulationSignaller*, bool, bool) [with gmx::ComputeGlobalsAlgorithm algorithm = gmx::ComputeGlobalsAlgorithm::LeapFrog]’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:284:20: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
284 | compute_globals(
| ~~~~~~~~~~~~~~~^
285 | gstat_, cr_, inputrec_, fr_, energyData_->ekindata(), x, v, box, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
286 | nrnb_, &vcm_, step != -1 ? wcycle_ : nullptr, energyData_->enerdata(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
287 | energyData_->forceVirial(step), energyData_->constraintVirial(step),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
288 | energyData_->totalVirial(step), energyData_->pressure(step), constr_, signaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
289 | lastbox, &totalNumberOfBondedInteractions_, energyData_->needToSumEkinhOld(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
290 | flags | (shouldCheckNumberOfBondedInteractions_ ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:284:20: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:291:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
291 | checkNumberOfBondedInteractions(mdlog_, cr_, totalNumberOfBondedInteractions_, top_global_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | localTopology_, x, box, &shouldCheckNumberOfBondedInteractions_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
295 | process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x, v);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp: In member function ‘void gmx::ComputeGlobalsElement<algorithm>::elementSetup() [with gmx::ComputeGlobalsAlgorithm algorithm = gmx::ComputeGlobalsAlgorithm::LeapFrog]’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
140 | process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
141 | v.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp: In member function ‘void gmx::ComputeGlobalsElement<algorithm>::compute(gmx::Step, unsigned int, gmx::SimulationSignaller*, bool, bool) [with gmx::ComputeGlobalsAlgorithm algorithm = gmx::ComputeGlobalsAlgorithm::VelocityVerlet]’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:284:20: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
284 | compute_globals(
| ~~~~~~~~~~~~~~~^
285 | gstat_, cr_, inputrec_, fr_, energyData_->ekindata(), x, v, box, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
286 | nrnb_, &vcm_, step != -1 ? wcycle_ : nullptr, energyData_->enerdata(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
287 | energyData_->forceVirial(step), energyData_->constraintVirial(step),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
288 | energyData_->totalVirial(step), energyData_->pressure(step), constr_, signaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
289 | lastbox, &totalNumberOfBondedInteractions_, energyData_->needToSumEkinhOld(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
290 | flags | (shouldCheckNumberOfBondedInteractions_ ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:284:20: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:291:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
291 | checkNumberOfBondedInteractions(mdlog_, cr_, totalNumberOfBondedInteractions_, top_global_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | localTopology_, x, box, &shouldCheckNumberOfBondedInteractions_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
295 | process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x, v);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:295:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp: In member function ‘void gmx::ComputeGlobalsElement<algorithm>::elementSetup() [with gmx::ComputeGlobalsAlgorithm algorithm = gmx::ComputeGlobalsAlgorithm::VelocityVerlet]’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
140 | process_and_stopcm_grp(fplog_, &vcm_, *mdAtoms_->mdatoms(), x.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
141 | v.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp:140:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp: In member function ‘void gmx::ConstraintsElement<variable>::apply(gmx::Step, bool, bool, bool) [with gmx::ConstraintVariable variable = gmx::ConstraintVariable::Positions]’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp:158:19: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
158 | constr_->apply(writeLog, writeEnergy, step, 1, 1.0, x, xprime, min_proj, statePropagatorData_->box(),
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
159 | lambdaBonded, &dvdlambda, v, calculateVirial, vir_con, variable);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp: In member function ‘void gmx::ConstraintsElement<variable>::apply(gmx::Step, bool, bool, bool) [with gmx::ConstraintVariable variable = gmx::ConstraintVariable::Velocities]’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp:158:19: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
158 | constr_->apply(writeLog, writeEnergy, step, 1, 1.0, x, xprime, min_proj, statePropagatorData_->box(),
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
159 | lambdaBonded, &dvdlambda, v, calculateVirial, vir_con, variable);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp: In function ‘bool ManCallBack(t_x11*, XEvent*, Window, void*)’:
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:367:46: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
367 | put_atoms_in_compact_unitcell(man->molw->pbcType, ecenterDEF, man->box, atomsArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:367:46: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function ‘void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int) [with bool doShellFC = true]’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:197:28: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
197 | relax_shell_flexcon(
| ~~~~~~~~~~~~~~~~~~~^
198 | fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
199 | pull_work_, step == nextNSStep_, static_cast<int>(flags), localTopology_, constr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | energyData_->enerdata(), statePropagatorData_->localNumAtoms(), x, v, box, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | hist, &forces, force_vir, mdAtoms_->mdatoms(), nrnb_, wcycle_, shellfc_, fr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
202 | runScheduleWork_, time, energyData_->muTot(), vsite_, ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function ‘void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int) [with bool doShellFC = false]’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:211:17: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
211 | do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
212 | nrnb_, wcycle_, localTopology_, box, x, hist, &forces, force_vir,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
213 | mdAtoms_->mdatoms(), energyData_->enerdata(), lambda, fr_, runScheduleWork_, vsite_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
214 | energyData_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energydata.cpp: In member function ‘void gmx::EnergyData::doStep(gmx::Time, bool, bool)’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energydata.cpp:241:42: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
241 | accumulateKineticLambdaComponents(enerd_, freeEnergyPerturbationData_->constLambdaView(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
242 | *inputrec_->fepvals);
| ~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp: In constructor ‘gmx::FreeEnergyPerturbationData::FreeEnergyPerturbationData(FILE*, const t_inputrec*, gmx::MDAtoms*)’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp:75:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
75 | initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp: In member function ‘void gmx::PmeLoadBalanceHelper::run(gmx::Step, gmx::Time)’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp:108:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
108 | pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
111 | step - inputrec_->init_step, &bPMETunePrinting_, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/simulatoralgorithm.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 7%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++17 -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function ‘void gmx::StatePropagatorData::Element::_ZN3gmx19StatePropagatorData7Element24trajectoryWriterTeardownEP10gmx_mdoutf.part.0(gmx_mdoutf*)’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:605:23: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
605 | dd_collect_vec(cr_->dd, localStateBackup_->ddp_count, localStateBackup_->ddp_count_cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
606 | localStateBackup_->cg_gl, localStateBackup_->x, globalXRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:605:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:609:23: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
609 | dd_collect_vec(cr_->dd, localStateBackup_->ddp_count, localStateBackup_->ddp_count_cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
610 | localStateBackup_->cg_gl, localStateBackup_->v, globalVRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:609:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function ‘void gmx::StatePropagatorData::Element::write(gmx_mdoutf_t, gmx::Step, gmx::Time)’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:440:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
440 | mdoutf_write_to_trajectory_files(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
441 | fplog_, cr_, outf, static_cast<int>(mdof_flags), statePropagatorData_->totalNumAtoms_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
442 | currentStep, currentTime, localStateBackup_.get(), statePropagatorData_->globalState_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
443 | observablesHistory, statePropagatorData_->f_.view().force(), &dummyCheckpointDataHolder_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function ‘void gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<gmx::BasicVector<double> >) const’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:469:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
469 | inline void ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<RVec> values) const
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function ‘void gmx::CheckpointData<gmx::CheckpointDataOperation::Write>::arrayRef(const string&, gmx::ArrayRef<const gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:485:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
485 | inline void WriteCheckpointData::arrayRef(const std::string& key, ArrayRef<const RVec> values)
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function ‘virtual void gmx::StatePropagatorData::Element::saveCheckpointState(std::optional<gmx::CheckpointData<gmx::CheckpointDataOperation::Write> >, const t_commrec*)’:
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:510:23: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
510 | dd_collect_vec(cr->dd, statePropagatorData_->ddpCount_, statePropagatorData_->ddpCountCgGl_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
511 | statePropagatorData_->cgGl_, statePropagatorData_->x_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | statePropagatorData_->xGlobal_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:510:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:513:23: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
513 | dd_collect_vec(cr->dd, statePropagatorData_->ddpCount_, statePropagatorData_->ddpCountCgGl_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | statePropagatorData_->cgGl_, statePropagatorData_->v_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | statePropagatorData_->vGlobal_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:513:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::StatePropagatorData::setLocalState(std::unique_ptr<t_state>)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::StatePropagatorData::doCheckpointData(gmx::CheckpointData<operation>*) [with gmx::CheckpointDataOperation operation = gmx::CheckpointDataOperation::Read]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::StatePropagatorData::Element::restoreCheckpointState(std::optional<gmx::CheckpointData<gmx::CheckpointDataOperation::Read> >, const t_commrec*)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘gmx::StatePropagatorData::StatePropagatorData(int, FILE*, const t_commrec*, t_state*, bool, bool, bool, const string&, const t_inputrec*, const t_mdatoms*, const gmx_mtop_t*)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 9%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp:77:
/<<PKGBUILDDIR>>/build/basic-dp/src/buildinfo.h:75: warning: "HWLOC_VERSION" redefined
75 | #define HWLOC_VERSION "2.4.0"
|
In file included from /usr/include/hwloc.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp:64:
/usr/include/arm-linux-gnueabihf/hwloc/autogen/config.h:15: note: this is the location of the previous definition
15 | #define HWLOC_VERSION "2.4.1"
|
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function ‘void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t&, gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:1471:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1471 | void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function ‘void nbnxn_atomdata_init(const gmx::MDLogger&, nbnxn_atomdata_t*, Nbnxm::KernelType, int, int, gmx::ArrayRef<const double>, int, int)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:623:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
623 | void nbnxn_atomdata_init(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp: In function ‘void Nbnxm::setupAndRunInstance(const gmx::BenchmarkSystem&, const Nbnxm::KernelBenchOptions&, bool)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:208:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
208 | nbnxn_atomdata_init(gmx::MDLogger(), nbv->nbat.get(), kernelSetup.kernelType, combinationRule,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
209 | system.numAtomTypes, system.nonbondedParameters, 1, numThreads);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:229:22: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
229 | nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
230 | { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
231 | system.coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:235:27: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
235 | nbv->setAtomProperties(system.atomTypes, system.charges, atomInfo);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:235:27: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function ‘void Nbnxm::Grid::fillCell(Nbnxm::GridSetData*, nbnxn_atomdata_t*, int, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, Nbnxm::BoundingBox*)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:860:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
860 | void Grid::fillCell(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function ‘void Nbnxm::Grid::sortColumnsCpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:988:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
988 | void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1028:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1028 | fillCell(gridSetData, nbat, atomOffsetCell, atomOffsetCell + numAtomsCell, atinfo, x, nullptr);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function ‘void Nbnxm::Grid::sortColumnsGpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1051:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1051 | void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1152:29: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1152 | fillCell(gridSetData, nbat, atomOffsetX, atomOffsetX + numAtomsX, atinfo, x,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1153 | bb_work_aligned);
| ~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function ‘void nbnxn_atomdata_set(nbnxn_atomdata_t*, const Nbnxm::GridSet&, gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, gmx::ArrayRef<const int>)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:955:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
955 | void nbnxn_atomdata_set(nbnxn_atomdata_t* nbat,
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:51:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Nbnxm::KernelBenchOptions&}; _Tp = Nbnxm::KernelBenchOptions; _Alloc = std::allocator<Nbnxm::KernelBenchOptions>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Nbnxm::KernelBenchOptions>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:51:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void Nbnxm::bench(int, const Nbnxm::KernelBenchOptions&)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In function ‘_ZN5Nbnxm4Grid14setCellIndicesEiiPNS_11GridSetDataEN3gmx8ArrayRefINS_8GridWorkEEENS3_5RangeIiEEPKiNS4_IKNS3_11BasicVectorIdEEEEiP16nbnxn_atomdata_t._omp_fn.0’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1410:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1410 | sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1411 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1405:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1405 | sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1406 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In static member function ‘static void Nbnxm::Grid::calcColumnIndices(const Nbnxm::Grid::Dimensions&, const gmx::UpdateGroupsCog*, gmx::Range<int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, int, gmx::ArrayRef<int>, gmx::ArrayRef<int>)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1173:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1173 | void Grid::calcColumnIndices(const Grid::Dimensions& gridDims,
| ^~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function ‘void Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, gmx::ArrayRef<Nbnxm::GridWork>, gmx::Range<int>, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1287:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1287 | void Grid::setCellIndices(int ddZone,
| ^~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In function ‘_ZN5Nbnxm7GridSet9putOnGridEPA3_KdiPS1_S4_PKN3gmx15UpdateGroupsCogENS5_5RangeIiEEdNS5_8ArrayRefIKiEENSB_IKNS5_11BasicVectorIdEEEEiPSC_P16nbnxn_atomdata_t._omp_fn.0’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:215:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
215 | Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
216 | nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In member function ‘void Nbnxm::GridSet::putOnGrid(const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, nbnxn_atomdata_t*)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:135:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
135 | void GridSet::putOnGrid(const matrix box,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:222:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
222 | grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
223 | numAtomsMoved, nbat);
| ~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function ‘void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality, const interaction_const_t&, const gmx::StepWorkload&, int, const t_forcerec&, gmx_enerdata_t*, t_nrnb*)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:446:33: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
446 | nbnxn_kernel_gpu_ref(
| ~~~~~~~~~~~~~~~~~~~~^
447 | pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
448 | nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
449 | fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function ‘void nonbonded_verlet_t::dispatchFreeEnergyKernel(gmx::InteractionLocality, const t_forcerec*, real (*)[3], gmx::ForceWithShiftForces*, const t_mdatoms&, t_lambda*, gmx::ArrayRef<const double>, gmx_enerdata_t*, const gmx::StepWorkload&, t_nrnb*)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:458:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
458 | void nonbonded_verlet_t::dispatchFreeEnergyKernel(gmx::InteractionLocality iLocality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp: In function ‘void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu*, const nbnxn_atomdata_t*, const interaction_const_t*, real (*)[3], const gmx::StepWorkload&, int, gmx::ArrayRef<double>, real*, real*, real*)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:58:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
58 | void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function ‘void nbnxn_put_on_grid(nonbonded_verlet_t*, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:58:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
58 | void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:54:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:197:27: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
197 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
198 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function ‘void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*, const gmx_domdec_zones_t*, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:77:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
77 | void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:91:26: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
91 | nbnxn_put_on_grid(nbv, nullptr, zone, c0, c1, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
92 | { zones->cg_range[zone], zones->cg_range[zone + 1] }, -1, atomInfo, x, 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
93 | nullptr);
| ~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function ‘void nonbonded_verlet_t::setAtomProperties(gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, gmx::ArrayRef<const int>)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:122:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
122 | void nonbonded_verlet_t::setAtomProperties(gmx::ArrayRef<const int> atomTypes,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:122:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:23: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
126 | nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), atomTypes, atomCharges, atomInfo);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function ‘void nonbonded_verlet_t::convertCoordinates(gmx::AtomLocality, bool, gmx::ArrayRef<const gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:129:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
129 | void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function ‘void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(gmx::AtomLocality, gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:162:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
162 | void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp: In function ‘std::unique_ptr<nonbonded_verlet_t> Nbnxm::init_nb_verlet(const gmx::MDLogger&, const t_inputrec*, const t_forcerec*, const t_commrec*, const gmx_hw_info_t&, bool, const gmx::DeviceStreamManager*, const gmx_mtop_t*, real (*)[3], gmx_wallcycle*)’:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp:431:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
431 | nbnxn_atomdata_init(mdlog, nbat.get(), kernelSetup.kernelType, enbnxninitcombrule, fr->ntype,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
432 | fr->nbfp, mimimumNumEnergyGroupNonbonded,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
433 | (useGpuForNonbonded || emulateGpu) ? 1 : gmx_omp_nthreads_get(emntNonbonded));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/11/bits/stl_vector.h: In function ‘_ZN11PairlistSet18constructPairlistsERKN5Nbnxm7GridSetEN3gmx8ArrayRefI14PairsearchWorkEEP16nbnxn_atomdata_tRKNS4_11ListOfListsIiEEiP6t_nrnbP19SearchCycleCounting._omp_fn.0’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void PairlistSet::constructPairlists(const Nbnxm::GridSet&, gmx::ArrayRef<PairsearchWork>, nbnxn_atomdata_t*, const gmx::ListOfLists<int>&, int, t_nrnb*, SearchCycleCounting*)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:39:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::PinningPolicy}; _Tp = NbnxnPairlistGpu; _Alloc = std::allocator<NbnxnPairlistGpu>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<NbnxnPairlistGpu>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In constructor ‘PairlistSet::PairlistSet(gmx::InteractionLocality, const PairlistParams&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function ‘void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, tmpi_comm_* const*, gmx_ddbox_t*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:233:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
233 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function ‘void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:279:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
279 | void set_ddbox(const gmx_domdec_t& dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:292:22: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
292 | low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.numCells,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | box, calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:292:22: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function ‘void set_ddbox_cr(DDRole, MPI_Comm, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:303:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
303 | void set_ddbox_cr(DDRole ddRole,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:313:22: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
313 | low_set_ddbox(numPbcDimensions(ir.pbcType), inputrec2nboundeddim(&ir), dd_nc, box, true, x,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
314 | nullptr, ddbox);
| ~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function ‘void dd_collect_vec(gmx_domdec_t*, int, int, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:231:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
231 | void dd_collect_vec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:231:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function ‘void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
296 | dd_collect_vec(dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | state_local->x, globalXRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:302:23: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
302 | dd_collect_vec(dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
303 | state_local->v, globalVRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:302:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:308:23: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
308 | dd_collect_vec(dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
309 | state_local->cg_p, globalCgpRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:308:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function ‘void distributeVec(gmx_domdec_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
143 | static void distributeVec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function ‘void distributeState(const gmx::MDLogger&, gmx_domdec_t*, const gmx_mtop_t&, t_state*, const gmx_ddbox_t&, t_state*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:256:22: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
256 | distributeVec(dd, DDMASTER(dd) ? state->x : gmx::ArrayRef<const gmx::RVec>(), state_local->x);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:256:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:256:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:260:22: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
260 | distributeVec(dd, DDMASTER(dd) ? state->v : gmx::ArrayRef<const gmx::RVec>(), state_local->v);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:260:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:260:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:264:22: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
264 | distributeVec(dd, DDMASTER(dd) ? state->cg_p : gmx::ArrayRef<const gmx::RVec>(), state_local->cg_p);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:264:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:264:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function ‘void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
118 | void ddSendrecv(const gmx_domdec_t* dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function ‘void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp: In function ‘void dd_move_x_constraints(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp:106:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
106 | void dd_move_x_constraints(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp:106:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function ‘gmx_bool test_dd_cutoff(const t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3074:17: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
3074 | static gmx_bool test_dd_cutoff(const t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3083:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
3083 | set_ddbox(*dd, false, box, true, x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function ‘gmx_bool change_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3140:10: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
3140 | gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function ‘void putUpdateGroupAtomsInSamePeriodicImage(const gmx_domdec_t&, const gmx_mtop_t&, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3225:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
3225 | void putUpdateGroupAtomsInSamePeriodicImage(const gmx_domdec_t& dd,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp: In function ‘DDGridSetup getDDGridSetup(const gmx::MDLogger&, DDRole, MPI_Comm, int, const gmx::DomdecOptions&, const DDSettings&, const DDSystemInfo&, real, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:891:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
891 | DDGridSetup getDDGridSetup(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:912:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
912 | set_ddbox_cr(ddRole, communicator, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:916:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
916 | set_ddbox_cr(ddRole, communicator, nullptr, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor ‘gmx::DomainDecompositionBuilder::Impl::Impl(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2967:1: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2967 | DomainDecompositionBuilder::Impl::Impl(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2167:38: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2167 | dd_bonded_cg_distance(mdlog, &mtop, &ir, xGlobal, box,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2168 | options.checkBondedInteractions, &r_2b, &r_mb);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2167:38: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3006:27: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
3006 | getDDGridSetup(mdlog_, MASTER(cr_) ? DDRole::Master : DDRole::Agent,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | cr->mpiDefaultCommunicator, numRanksRequested, options_, ddSettings_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | systemInfo_, gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor ‘gmx::DomainDecompositionBuilder::DomainDecompositionBuilder(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3053:1: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
3053 | DomainDecompositionBuilder::DomainDecompositionBuilder(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3061:76: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
3061 | impl_(new Impl(mdlog, cr, options, mdrunOptions, mtop, ir, box, xGlobal))
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function ‘void dd_atom_spread_real(gmx_domdec_t*, real*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:519:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
519 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:519:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:519:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp: In function ‘void dd_print_missing_interactions(const gmx::MDLogger&, t_commrec*, int, const gmx_mtop_t*, const gmx_localtop_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3])’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:364:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
364 | void dd_print_missing_interactions(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function ‘void dd_atom_sum_real(gmx_domdec_t*, real*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:583:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
583 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:583:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:583:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function ‘void dd_move_x(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:260:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
260 | void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:337:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
337 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:337:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:337:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function ‘void dd_move_f(gmx_domdec_t*, gmx::ForceWithShiftForces*, gmx_wallcycle*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:412:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
412 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:412:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:412:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp: In function ‘void dd_bonded_cg_distance(const gmx::MDLogger&, const gmx_mtop_t*, const t_inputrec*, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3], gmx_bool, real*, real*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:1991:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1991 | void dd_bonded_cg_distance(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp: In function ‘void dd_move_f_vsites(const gmx_domdec_t&, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp:69:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
69 | void dd_move_f_vsites(const gmx_domdec_t& dd, gmx::ArrayRef<gmx::RVec> f, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp:69:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp: In function ‘void dd_clear_f_vsites(const gmx_domdec_t&, gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp:77:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
77 | void dd_clear_f_vsites(const gmx_domdec_t& dd, gmx::ArrayRef<gmx::RVec> f)
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:53:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const t_iparams*, std::vector<t_iparams> >; <template-parameter-2-2> = void; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]’:
/usr/include/c++/11/bits/stl_vector.h:1379:9: note: parameter passing for argument of type ‘std::vector<t_iparams>::const_iterator’ changed in GCC 7.1
1379 | insert(const_iterator __position, _InputIterator __first,
| ^~~~~~
/usr/include/c++/11/bits/stl_vector.h:1379:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_vector.h:1379:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp: In function ‘void dd_make_local_top(gmx_domdec_t*, gmx_domdec_zones_t*, int, real (*)[3], real*, const int*, t_forcerec*, real (*)[3], const gmx_mtop_t&, gmx_localtop_t*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:1028:40: note: parameter passing for argument of type ‘std::vector<t_iparams>::const_iterator’ changed in GCC 7.1
1028 | iparams_dest.insert(iparams_dest.end(), iparams_src.begin(), iparams_src.end());
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:1028:40: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:53:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_iparams>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp:53:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void add_posres(int, int, int, const gmx_molblock_t*, t_iatom*, const t_iparams*, InteractionDefinitions*)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In function ‘void add_fbposres(int, int, int, const gmx_molblock_t*, t_iatom*, const t_iparams*, InteractionDefinitions*)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function ‘void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:254:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
254 | ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
255 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:254:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:254:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function ‘void checkNumberOfBondedInteractions(const gmx::MDLogger&, t_commrec*, int, const gmx_mtop_t*, const gmx_localtop_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3], bool*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3222:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
3222 | void checkNumberOfBondedInteractions(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3235:42: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
3235 | dd_print_missing_interactions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3236 | top_local, x, box); // Does not return
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function ‘void gmx::ScaleCoordinates::Impl::scale(gmx::ArrayRef<gmx::BasicVector<double> >) const’:
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:70:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
70 | void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function ‘void gmx::ScaleCoordinates::Impl::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const’:
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:80:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
80 | void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function ‘void gmx::ScaleCoordinates::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const’:
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
102 | void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:104:17: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
104 | impl_->scale(coordinates);
| ~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function ‘void gmx::ScaleCoordinates::operator()(gmx::RVec*) const’:
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:109:17: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
109 | impl_->scale({ coordinate, coordinate + 1 });
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function ‘void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const’:
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:112:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
112 | void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:112:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:114:36: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
114 | impl_->inverseIgnoringZeroScale(coordinates);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function ‘void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::RVec*) const’:
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:119:36: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
119 | impl_->inverseIgnoringZeroScale({ coordinate, coordinate + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function ‘void gmx::TranslateAndScale::Impl::transform(gmx::ArrayRef<gmx::BasicVector<double> >) const’:
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:155:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
155 | void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function ‘void gmx::TranslateAndScale::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const’:
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:176:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
176 | void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:178:21: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
178 | impl_->transform(coordinates);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function ‘void gmx::TranslateAndScale::operator()(gmx::RVec*) const’:
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:183:21: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
183 | impl_->transform({ coordinate, coordinate + 1 });
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In constructor ‘gmx::AffineTransformation::AffineTransformation(gmx::Matrix3x3ConstSpan, const RVec&)’:
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:211:1: note: parameter passing for argument of type ‘gmx::Matrix3x3ConstSpan’ {aka ‘gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >’} changed in GCC 7.1
211 | AffineTransformation::AffineTransformation(Matrix3x3ConstSpan matrix, const RVec& translation) :
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function ‘void gmx::AffineTransformation::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const’:
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:217:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
217 | void AffineTransformation::operator()(ArrayRef<RVec> vectors) const
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function ‘void gmx::AffineTransformation::operator()(gmx::RVec*) const’:
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:228:12: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
228 | (*this)({ vector, vector + 1 });
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function ‘void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2105:34: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
2105 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2105:34: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2105:34: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function ‘void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t&, const t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, gmx::ForceBuffers*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx::VirtualSitesHandler*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)’:
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2867:18: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2867 | set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2908:18: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2908 | set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2929:18: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2929 | set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2947:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2947 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2948 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2947:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2971:43: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2971 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2972 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2973 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2971:43: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3006:26: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
3006 | nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3009 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/neldermead.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp: In function ‘gmx::Matrix3x3 gmx::transpose(gmx::Matrix3x3ConstSpan)’:
/<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp:50:11: note: parameter passing for argument of type ‘gmx::Matrix3x3ConstSpan’ {aka ‘gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >’} changed in GCC 7.1
50 | Matrix3x3 transpose(Matrix3x3ConstSpan matrixView)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp: In function ‘void gmx::matrixVectorMultiply(gmx::Matrix3x3ConstSpan, gmx::RVec*)’:
/<<PKGBUILDDIR>>/src/gromacs/math/matrix.cpp:58:6: note: parameter passing for argument of type ‘gmx::Matrix3x3ConstSpan’ {aka ‘gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >’} changed in GCC 7.1
58 | void matrixVectorMultiply(Matrix3x3ConstSpan matrix, RVec* v)
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/optimization.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/optimization.cpp: In function ‘gmx::OptimisationResult gmx::nelderMead(const std::function<double(gmx::ArrayRef<const double>)>&, gmx::ArrayRef<const double>, real, int)’:
/<<PKGBUILDDIR>>/src/gromacs/math/optimization.cpp:51:20: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
51 | OptimisationResult nelderMead(const std::function<real(ArrayRef<const real>)>& functionToMinimize,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/neldermead.cpp: In constructor ‘gmx::NelderMeadSimplex::NelderMeadSimplex(const std::function<double(gmx::ArrayRef<const double>)>&, gmx::ArrayRef<const double>)’:
/<<PKGBUILDDIR>>/src/gromacs/math/neldermead.cpp:100:1: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
100 | NelderMeadSimplex::NelderMeadSimplex(const std::function<real(ArrayRef<const real>)>& f,
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/energyhistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcebuffers.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::ForceBuffers::resize(int)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/energyhistory.cpp:43:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function ‘std::enable_if_t<gmx::IsSerializableType<T>::value, void> gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<T>) const [with T = double]’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:442:1: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
442 | ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<T> values) const
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘gmx::ForceBuffers::ForceBuffers(bool, gmx::PinningPolicy)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘gmx::ForceBuffers::ForceBuffers()’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/interaction_const.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/multipletimestepping.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function ‘real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:270:7: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
270 | rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function ‘void printLambdaStateToLog(FILE*, gmx::ArrayRef<double>, bool)’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:344:6: note: parameter passing for argument of type ‘const gmx::ArrayRef<double>’ changed in GCC 7.1
344 | void printLambdaStateToLog(FILE* fplog, const gmx::ArrayRef<real> lambda, const bool isInitialOutput)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function ‘void initialize_lambdas(FILE*, const t_inputrec&, bool, int*, gmx::ArrayRef<double>)’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:357:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
357 | void initialize_lambdas(FILE* fplog, const t_inputrec& ir, bool isMaster, int* fep_state, gmx::ArrayRef<real> lambda)
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:407:26: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
407 | printLambdaStateToLog(fplog, lambda, isInitialOutput);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:63:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h: In member function ‘std::enable_if_t<gmx::IsSerializableType<T>::value, void> gmx::CheckpointData<gmx::CheckpointDataOperation::Read>::arrayRef(const string&, gmx::ArrayRef<T>) const [with T = double]’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/checkpointdata.h:442:1: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
442 | ReadCheckpointData::arrayRef(const std::string& key, ArrayRef<T> values) const
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void init_gtc_state(t_state*, int, int, int)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:41:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void state_change_natoms(t_state*, int)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp: In function ‘void gmx::shiftAtoms(const RVec&, gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:124:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
124 | void shiftAtoms(const RVec& shift, ArrayRef<RVec> x)
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp: In function ‘void gmx::placeCoordinatesWithCOMInBox(const PbcType&, gmx::UnitCellType, gmx::CenteringType, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, const gmx_mtop_t&, gmx::COMShiftType)’:
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:129:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
129 | void placeCoordinatesWithCOMInBox(const PbcType& pbcType,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:86:42: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
86 | put_atoms_in_compact_unitcell(pbcType, static_cast<int>(centerType), box, comArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:86:42: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.cpp:163:27: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
163 | shiftAtoms(shift, coords);
| ~~~~~~~~~~^~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function ‘void put_atoms_in_box(PbcType, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1388:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1388 | void put_atoms_in_box(PbcType pbcType, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function ‘void put_atoms_in_box_omp(PbcType, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, int)’:
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1448:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1448 | void put_atoms_in_box_omp(PbcType pbcType, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function ‘void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1464:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1464 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function ‘void put_atoms_in_compact_unitcell(PbcType, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1521:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1521 | void put_atoms_in_compact_unitcell(PbcType pbcType, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1521:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function ‘void put_molecule_com_in_box(int, int, t_block*, int, t_atom*, PbcType, real (*)[3], real (*)[3])’:
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
289 | put_atoms_in_compact_unitcell(pbcType, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function ‘void put_residue_com_in_box(int, int, int, t_atom*, PbcType, real (*)[3], real (*)[3])’:
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:347:50: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
347 | put_atoms_in_compact_unitcell(pbcType, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:347:50: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor ‘gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)’:
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor ‘gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)’:
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:368:1: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
368 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function ‘real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)’:
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function ‘real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)’:
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function ‘void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)’:
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function ‘std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)’:
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BaseEntry}; _Tp = BaseEntry; _Alloc = std::allocator<BaseEntry>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<BaseEntry>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘void readProperty(AtomProperty*, ResidueType*, double)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<swap_group>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘t_swap* init_swapcoords(FILE*, const t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.h:54,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<edpar>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘std::unique_ptr<gmx::EssentialDynamics> ed_open(int, ObservablesHistory*, const char*, const char*, gmx::StartingBehavior, const gmx_output_env_t*, const t_commrec*)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<pull_coord_work_t>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<pull_group_work_t>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<pull_group_work_t>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type ‘std::vector<pull_group_work_t>::iterator’ changed in GCC 7.1
2297 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type ‘std::vector<pull_group_work_t>::iterator’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type ‘std::vector<pull_group_work_t>::iterator’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2297:1: note: parameter passing for argument of type ‘std::vector<pull_group_work_t>::iterator’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function ‘bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)’:
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:944:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
944 | bool pullCheckPbcWithinGroup(const pull_t& pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:944:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void allocStatePrevStepPullCom(t_state*, const pull_t*)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:50:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:50:
/usr/include/c++/11/bits/stl_vector.h: In function ‘int gmx_awh(int, char**)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_mapping>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘int strip_dssp(FILE*, int, const gmx_bool*, real, real*, FILE*, t_matrix*, int*, const gmx_output_env_t*)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In function ‘void prune_ss_legend(t_matrix*)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_gyrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_h2order.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hbond.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helixorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hydorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_lie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_make_edi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mdmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmeig.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘t_corr::t_corr(int, int, int, real, int, gmx_bool, gmx_bool, real, const t_topology*, real, real)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmens.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_order.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_polystat.cpp
/usr/include/c++/11/bits/vector.tcc: In function ‘int gmx_nmtraj(int, char**)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_potential.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_principal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rama.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotacf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saltbr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sans.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saxs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sigeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spatial.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tcaf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘gmx::BenchmarkSystem::BenchmarkSystem(int, const string&)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function ‘void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1329:13: note: parameter passing for argument of type ‘gmx::ArrayRef<t_mapping>’ changed in GCC 7.1
1329 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function ‘void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:250:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
250 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function ‘void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1034:31: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
1034 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1035 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1034:31: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
317 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:318:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
318 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:318:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function ‘int gmx_xpm2ps(int, char**)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1377:20: note: parameter passing for argument of type ‘gmx::ArrayRef<t_mapping>’ changed in GCC 7.1
1377 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1377:20: note: parameter passing for argument of type ‘gmx::ArrayRef<t_mapping>’ changed in GCC 7.1
1377 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function ‘double calcZeroPointEnergy(gmx::ArrayRef<const double>, real)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:53:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
53 | double calcZeroPointEnergy(gmx::ArrayRef<const real> eigval, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function ‘double calcVibrationalInternalEnergy(gmx::ArrayRef<const double>, real, gmx_bool, real)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:66:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
66 | double calcVibrationalInternalEnergy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function ‘double calcVibrationalHeatCapacity(gmx::ArrayRef<const double>, real, gmx_bool, real)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:93:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
93 | double calcVibrationalHeatCapacity(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function ‘double calcQuasiHarmonicEntropy(gmx::ArrayRef<const double>, real, gmx_bool, real)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:158:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
158 | double calcQuasiHarmonicEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function ‘double calcSchlitterEntropy(gmx::ArrayRef<const double>, real, gmx_bool)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:185:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
185 | double calcSchlitterEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear)
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<InteractionOfType>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function ‘void add_param(InteractionsOfType*, int, int, gmx::ArrayRef<const double>, const char*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:56:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
56 | void add_param(InteractionsOfType* ps, int ai, int aj, gmx::ArrayRef<const real> c, const char* s)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:65:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
65 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm, s ? s : ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:65:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function ‘void add_vsite4_atoms(InteractionsOfType*, int, int, int, int, int)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:102:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
102 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:102:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function ‘void add_vsite3_atoms(InteractionsOfType*, int, int, int, int, bool)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:91:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
91 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:91:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function ‘void add_cmap_param(InteractionsOfType*, int, int, int, int, int, const char*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:71:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
71 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}, s ? s : ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:71:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function ‘void add_vsite2_param(InteractionsOfType*, int, int, int, real)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:78:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
78 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:78:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function ‘void add_vsite3_param(InteractionsOfType*, int, int, int, int, real, real)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:85:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
85 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:85:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:45:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:50:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_iparams>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:50:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In function ‘void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<InteractionOfType>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<InteractionOfType, int>}; _Tp = std::pair<InteractionOfType, int>; _Alloc = std::allocator<std::pair<InteractionOfType, int> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<std::pair<InteractionOfType, int> >::iterator’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function ‘std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType>, gmx::ArrayRef<const InteractionOfType>, t_atoms*, bool, bool)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:233:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const InteractionOfType>’ changed in GCC 7.1
233 | static std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType> dih,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:233:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const InteractionOfType>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<InteractionOfType>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]’:
/usr/include/c++/11/bits/stl_algo.h:1861:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1861 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1861:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1861:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function ‘int gen_vsites_6ring(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, real, real, real, bool)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]’:
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]’:
/usr/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]’:
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]’:
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/stl_heap.h:424:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1646:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1646 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function ‘int gen_vsites_his(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, gmx::ArrayRef<const VirtualSiteTopology>)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function ‘void gen_pad(t_atoms*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<InteractionsOfType>, t_excls*, gmx::ArrayRef<MoleculePatchDatabase>, bool, gmx::ArrayRef<const int>)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
674 | ang.push_back(InteractionOfType(atomNumbers, {}, name));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:63: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
725 | dih.push_back(InteractionOfType(atomNumbers, {}, name));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:63: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:51: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
735 | dih.push_back(InteractionOfType(atoms, {}, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:51: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:59: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
754 | pai.push_back(InteractionOfType(atoms, {}, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:59: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:822:35: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
822 | ang.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:822:35: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:875:35: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
875 | dih.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:875:35: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1957:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1957 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1957:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1957 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1957:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1957 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:372:43: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
372 | improper.emplace_back(InteractionOfType(ai, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:372:43: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:916:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const InteractionOfType>’ changed in GCC 7.1
916 | dih = clean_dih(dih, improper, atoms, rtpFFDB[0].bKeepAllGeneratedDihedrals,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
917 | rtpFFDB[0].bRemoveDihedralIfWithImproper);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:916:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const InteractionOfType>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:916:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const InteractionOfType>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:48:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<MoleculePatch>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void expand_hackblocks_one(const MoleculePatchDatabase&, std::string, std::vector<MoleculePatch>*, bool, bool)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function ‘int gen_vsites_tyr(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genion.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function ‘int gen_vsites_trp(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function ‘void do_vsites(gmx::ArrayRef<const PreprocessResidue>, PreprocessingAtomTypes*, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, gmx::ArrayRef<InteractionsOfType>, int**, int**, real, bool, const char*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
638 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:638:14: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2248:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
2248 | *parm = InteractionOfType(newAtomNumber, parm->forceParam(), parm->interactionTypeName());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2248:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:46:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&, char**, const InteractionOfType&, int&, int&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<AtomTypeData>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
/usr/include/c++/11/bits/vector.tcc: In member function ‘int PreprocessingAtomTypes::addType(t_symtab*, const t_atom&, const string&, const InteractionOfType&, int, int)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<InteractionOfType>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/11/bits/c++allocator.h:33,
from /usr/include/c++/11/bits/allocator.h:46,
from /usr/include/c++/11/string:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:40:
/usr/include/c++/11/ext/new_allocator.h:162:11: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/ext/new_allocator.h:162:11: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:46:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const AtomTypeData&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<AtomTypeData>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/11/bits/c++allocator.h:33,
from /usr/include/c++/11/bits/allocator.h:46,
from /usr/include/c++/11/string:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:40:
/usr/include/c++/11/ext/new_allocator.h: In member function ‘void PreprocessingAtomTypes::renumberTypes(gmx::ArrayRef<InteractionsOfType>, gmx_mtop_t*, int*, bool)’:
/usr/include/c++/11/ext/new_allocator.h:162:11: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/ext/new_allocator.h:162:11: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:46:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:46:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:41:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_atom>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/string:40,
from /usr/include/c++/11/bits/locale_classes.h:40,
from /usr/include/c++/11/bits/ios_base.h:41,
from /usr/include/c++/11/streambuf:41,
from /usr/include/c++/11/bits/streambuf_iterator.h:35,
from /usr/include/c++/11/iterator:66,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:54,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:41:
In static member function ‘static constexpr std::size_t std::char_traits<char>::length(const char_type*)’,
inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::assign(const _CharT*) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/11/bits/basic_string.h:1458:19,
inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(const _CharT*) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/11/bits/basic_string.h:689:28,
inlined from ‘void read_ab(char*, const char*, MoleculePatch*)’ at /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:115:25:
/usr/include/c++/11/bits/char_traits.h:371:32: warning: ‘unsigned int __builtin_strlen(const char*)’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
371 | return __builtin_strlen(__s);
| ~~~~~~~~~~~~~~~~^~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp: In function ‘void read_ab(char*, const char*, MoleculePatch*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:88:10: note: at offset 48 into source object ‘a’ of size 48
88 | char a[4][12];
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp: In constructor ‘InteractionOfType::InteractionOfType(gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const string&)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp:114:1: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
114 | InteractionOfType::InteractionOfType(gmx::ArrayRef<const int> atoms,
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:41:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void copyPreprocessResidues(const PreprocessResidue&, PreprocessResidue*, t_symtab*)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:41:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<MoleculePatch>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:41:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void mergeAtomModifications(const MoleculePatchDatabase&, MoleculePatchDatabase*)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp: In function ‘void insert_mols(int, int, int, real, real, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, const std::set<int>&, const t_atoms&, gmx::ArrayRef<gmx::BasicVector<double> >, PbcType, real (*)[3], const string&, const real*, RotationType)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:171:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
171 | static void insert_mols(int nmol_insrt,
| ^~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:38:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:38:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::vector<double> makeExclusionDistances(const t_atoms*, AtomProperties*, real, real)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:41:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<MoleculePatch>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘void read_h_db_file(const char*, std::vector<MoleculePatchDatabase>*)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp: In member function ‘virtual int gmx::{anonymous}::InsertMolecules::run()’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:589:16: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
589 | insert_mols(nmolIns_, nmolTry_, seed_, defaultDistance_, scaleFactor_, &atoms, &top_.symtab,
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
590 | &x_, removableAtoms, atomsInserted, xInserted, pbcTypeForOutput, box_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
591 | positionFile_, deltaR_, enumRot_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp: In function ‘int nm2type(int, t_nm2type*, t_symtab*, t_atoms*, PreprocessingAtomTypes*, int*, InteractionsOfType*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:343:63: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
343 | k = atype->addType(tab, atoms->atom[i], type, InteractionOfType({}, {}),
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:343:63: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_atom>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function ‘void process_pull_groups(gmx::ArrayRef<t_pull_group>, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const t_blocka*, char**)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:453:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘gmx::index’ {aka ‘int’} [-Wformat=]
453 | "Number of weights (%ld) for pull group %d '%s' does not match the number of "
| ~~^
| |
| long int
| %d
454 | "atoms (%ld)",
455 | gmx::ssize(pullGroup.weight), g, pullGroupNames[g].c_str(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| gmx::index {aka int}
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:454:33: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 8 has type ‘gmx::index’ {aka ‘int’} [-Wformat=]
454 | "atoms (%ld)",
| ~~^
| |
| long int
| %d
455 | gmx::ssize(pullGroup.weight), g, pullGroupNames[g].c_str(),
456 | gmx::ssize(pullGroup.ind));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| gmx::index {aka int}
/usr/include/c++/11/bits/vector.tcc: In function ‘void add_atom_to_restp(PreprocessResidue*, t_symtab*, int, const MoleculePatch*)’:
/usr/include/c++/11/bits/vector.tcc:161:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >’ changed in GCC 7.1
161 | _M_realloc_insert(begin() + (__position - cbegin()), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function ‘void checkPullCoords(gmx::ArrayRef<const t_pull_group>, gmx::ArrayRef<const t_pull_coord>)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:484:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_pull_coord>’ changed in GCC 7.1
484 | void checkPullCoords(gmx::ArrayRef<const t_pull_group> pullGroups, gmx::ArrayRef<const t_pull_coord> pullCoords)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function ‘pull_t* set_pull_init(t_inputrec*, const gmx_mtop_t*, real (*)[3], real (*)[3], real, warninp_t)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:546:53: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
546 | bool groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
547 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
548 | pbc, g, c_pullGroupSmallGroupThreshold);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:577:52: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
577 | groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
578 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
579 | pbc, g, c_pullGroupPbcMargin);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = t_pull_coord; _Alloc = std::allocator<t_pull_coord>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_pull_coord>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::vector<std::__cxx11::basic_string<char> > read_pullparams(std::vector<t_inpfile>*, pull_params_t*, warninp_t)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:45:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_pull_coord*, std::vector<t_pull_coord> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function ‘void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, t_atoms*, t_symtab*, gmx::ArrayRef<gmx::BasicVector<double> >, bool, const gmx::MDLogger&)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:1335:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1335 | void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue> usedPpResidues,
| ^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:40:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void {anonymous}::sort_pdbatoms(gmx::ArrayRef<const PreprocessResidue>, int, t_atoms**, t_atoms**, std::vector<gmx::BasicVector<double> >*, t_blocka*, char***)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]’:
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]’:
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]’:
/usr/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]’:
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]’:
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/11/bits/stl_heap.h:424:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1646:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1646 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function ‘void pdb2top(FILE*, const char*, const char*, t_atoms*, std::vector<gmx::BasicVector<double> >*, PreprocessingAtomTypes*, t_symtab*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, bool, bool, bool, const char*, real, gmx::ArrayRef<const DisulfideBond>, real, real, bool, bool, bool, bool, bool, gmx::ArrayRef<const int>, const gmx::MDLogger&)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:808:26: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
808 | add_param(psb, ai, aj, {}, patch.s.c_str());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:808:26: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:822:38: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
822 | add_param(psb, i, i + 1, {}, nullptr); /* C-O */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:822:38: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:823:38: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
823 | add_param(psb, i, i + 2, {}, nullptr); /* C-OA */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:823:38: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:824:38: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
824 | add_param(psb, i + 2, i + 3, {}, nullptr); /* OA-H */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:824:38: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:829:42: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
829 | add_param(psb, i, i + k + 1, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:829:42: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:749:18: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
749 | add_param(ps, ai, aj, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:749:18: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:40:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual int gmx::{anonymous}::pdb2gmx::run()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:2399:33: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
2399 | match_atomnames_with_rtp(restp_chain, hb_chain, pdba, &symtab, x, bVerbose_, logger);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:40:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/11/bits/vector.tcc: In function ‘void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/11/bits/stl_vector.h: In function ‘int gmx_solvate(int, char**)’:
/usr/include/c++/11/bits/stl_vector.h:1665:26: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1665:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_vector.h:1665:26: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1665:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp: In function ‘PreprocessingAtomTypes read_atype(const char*, t_symtab*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:95:43: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
95 | at.addType(tab, *a, name, InteractionOfType({}, {}), 0, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:95:43: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_atom>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SpecialBond&}; _Tp = SpecialBond; _Alloc = std::allocator<SpecialBond>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<SpecialBond>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:40:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::vector<SpecialBond> generateSpecialBonds()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SpecialBond*, std::vector<SpecialBond> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:49:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<InteractionOfType>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘void readResidueDatabase(const string&, std::vector<PreprocessResidue>*, PreprocessingAtomTypes*, t_symtab*, const gmx::MDLogger&, bool)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp: In function ‘void convert_harmonics(gmx::ArrayRef<MoleculeInformation>, PreprocessingAtomTypes*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:232:33: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
232 | InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:232:33: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:49:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<MoleculePatch>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_atom>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘void read_ter_db_file(const char*, std::vector<MoleculePatchDatabase>*, PreprocessingAtomTypes*)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]’:
/usr/include/c++/11/bits/vector.tcc:171:5: note: parameter passing for argument of type ‘std::vector<InteractionOfType>::iterator’ changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp: In function ‘void make_shake(gmx::ArrayRef<InteractionsOfType>, t_atoms*, int, const gmx::MDLogger&)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:185:59: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
185 | InteractionOfType(atomNumbers, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:185:59: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1431:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:217:63: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
217 | add_param_to_list(&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:217:63: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp_impl.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1431:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<InteractionOfType>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp: In function ‘void print_bondeds(FILE*, int, Directive, int, int, gmx::ArrayRef<const InteractionsOfType>)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:341:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
341 | atype.addType(&stab, *a, buf, InteractionOfType({}, {}), 0, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:341:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:46:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<InteractionOfType>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘void add_param_to_list(InteractionsOfType*, const InteractionOfType&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp: In function ‘char** read_topol(const char*, const char*, const char*, const char*, t_symtab*, PreprocessingAtomTypes*, std::vector<MoleculeInformation>*, std::unique_ptr<MoleculeInformation>*, gmx::ArrayRef<InteractionsOfType>, int*, double*, t_gromppopts*, real*, std::vector<gmx_molblock_t>*, bool*, bool, bool, bool, warninp*, const gmx::MDLogger&)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:137:46: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
137 | pairs->interactionTypes.emplace_back(InteractionOfType(atomNumbers, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:137:46: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:40:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function ‘void generate_LJCpairsNB(MoleculeInformation*, int, InteractionsOfType*, warninp*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2657:71: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
2657 | add_param_to_list(&mol->interactions[F_LJC_PAIRS_NB], InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2657:71: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function ‘void push_at(t_symtab*, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, int, t_nbparam***, t_nbparam***, warninp*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:542:57: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
542 | InteractionOfType interactionType({}, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:542:57: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function ‘void push_bond(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, bool, bool, real, bool, bool*, warninp*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1985:50: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1985 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1985:50: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function ‘bool calc_vsite3out_param(PreprocessingAtomTypes*, InteractionOfType*, t_atoms*, gmx::ArrayRef<const VsiteBondedInteraction>, gmx::ArrayRef<const VsiteBondedInteraction>)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:544:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const VsiteBondedInteraction>’ changed in GCC 7.1
544 | static bool calc_vsite3out_param(PreprocessingAtomTypes* atypes,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:544:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const VsiteBondedInteraction>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function ‘void push_cmap(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, warninp*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2337:64: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
2337 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2337:64: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function ‘void lo_set_force_const(InteractionsOfType*, real*, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:46:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VsiteBondedInteraction}; _Tp = VsiteBondedInteraction; _Alloc = std::allocator<VsiteBondedInteraction>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<VsiteBondedInteraction>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function ‘void push_vsitesn(Directive, gmx::ArrayRef<InteractionsOfType>, t_atoms*, char*, warninp*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2444:41: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
2444 | add_param_to_list(&bond[ftype], InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2444:41: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘void enter_bonded(int, std::vector<VsiteBondedInteraction>*, const InteractionOfType&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<VsiteBondedInteraction*, std::vector<VsiteBondedInteraction> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function ‘int add_atomtype_decoupled(t_symtab*, PreprocessingAtomTypes*, t_nbparam***, t_nbparam***)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2575:49: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
2575 | nr = at->addType(symtab, atom, "decoupled", InteractionOfType({}, forceParam, ""), -1, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2575:49: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<InteractionOfType>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function ‘void generate_nbparams(int, int, InteractionsOfType*, PreprocessingAtomTypes*, warninp*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:104:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
104 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:104:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:128:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
128 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:128:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:152:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
152 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:152:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:185:65: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
185 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:185:65: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function ‘int gmx_x2top(int, char**)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:136:41: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
136 | add_param_to_list(bond, InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:136:41: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function ‘int set_vsites(bool, t_atoms*, PreprocessingAtomTypes*, gmx::ArrayRef<InteractionsOfType>, const gmx::MDLogger&)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:849:58: note: parameter passing for argument of type ‘gmx::ArrayRef<const VsiteBondedInteraction>’ changed in GCC 7.1
849 | bERROR = calc_vsite3out_param(atypes, ¶m, atoms, allVsiteBondeds.bonds,
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 | allVsiteBondeds.angles);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:849:58: note: parameter passing for argument of type ‘gmx::ArrayRef<const VsiteBondedInteraction>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:849:58: note: parameter passing for argument of type ‘gmx::ArrayRef<const VsiteBondedInteraction>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function ‘void push_bondtype(InteractionsOfType*, const InteractionOfType&, int, int, bool, const char*, warninp*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:712:17: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
712 | InteractionOfType(b.atoms(), b.forceParam(), b.interactionTypeName()));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:712:17: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:731:43: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
731 | bt->interactionTypes.emplace_back(InteractionOfType(atoms, forceParam, b.interactionTypeName()));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:731:43: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/xlate.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function ‘void push_bt(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:852:33: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
852 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:852:33: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function ‘void push_dihedraltype(Directive, gmx::ArrayRef<InteractionsOfType>, PreprocessingBondAtomType*, char*, warninp*)’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1020:33: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1020 | push_bondtype(&(bt[ftype]), InteractionOfType(atoms, forceParam), 4, ftype, bAllowRepeat, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1020:33: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘void push_cmaptype(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1287:33: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1287 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1287:33: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<InteractionOfType>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<InteractionOfType>::iterator’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp
/usr/include/c++/11/bits/vector.tcc: In function ‘void convert_pairs_to_pairsQ(gmx::ArrayRef<InteractionsOfType>, real, t_atoms*)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2607:31: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
2607 | paramnew.emplace_back(InteractionOfType(param.atoms(), forceParam, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2607:31: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:40:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:46:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<InteractionOfType>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]’:
/usr/include/c++/11/bits/vector.tcc:171:5: note: parameter passing for argument of type ‘std::vector<InteractionOfType>::iterator’ changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/crosscorr.cpp
/usr/include/c++/11/bits/vector.tcc: In function ‘void clean_vsite_bondeds(gmx::ArrayRef<InteractionsOfType>, int, bool, const gmx::MDLogger&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:46:
/usr/include/c++/11/bits/stl_vector.h:1431:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1431:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1431:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1431:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >’ changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void low_do_four_core(int, real*, real*, int)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/expfit.cpp
/usr/include/c++/11/bits/stl_vector.h: In function ‘void low_do_autocorr(const char*, const gmx_output_env_t*, const char*, int, int, int, real**, real, long unsigned int, int, gmx_bool, gmx_bool, gmx_bool, real, real, int)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/gmx_lmcurve.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/integrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/11/bits/stl_vector.h: In function ‘_Z16many_auto_correlPSt6vectorIS_IdSaIdEESaIS1_EE._omp_fn.0’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In function ‘int many_auto_correl(std::vector<std::vector<double> >*)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In constructor ‘gmx::AbstractAnalysisArrayData::AbstractAnalysisArrayData()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::AnalysisDataValue>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::AnalysisDataValue>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::AnalysisDataDisplacementModule::frameFinished(const gmx::AnalysisDataFrameHeader&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::AnalysisDataValue>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::AnalysisDataValue>::iterator’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function ‘void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef<const gmx::AnalysisDataValue>)’:
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:584:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::AnalysisDataValue>’ changed in GCC 7.1
584 | void AnalysisDataStorageFrameData::addPointSet(int dataSetIndex,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function ‘void gmx::AnalysisDataStorageFrame::finishPointSet()’:
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:715:27: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::AnalysisDataValue>’ changed in GCC 7.1
715 | data_->addPointSet(currentDataSet_, firstColumn,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
716 | makeConstArrayRef(values_).subArray(begin, end - begin));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:715:27: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::AnalysisDataValue>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/coordinatefile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/outputselector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setforces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setprecision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:45:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:48:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:48:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::analysismodules::{anonymous}::Sasa::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/eneconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/make_ndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/mk_angndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/pme_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjcat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tune_pme.cpp
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp: In function ‘int gmx_trjconv(int, char**)’:
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1246:66: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1246 | put_atoms_in_compact_unitcell(pbcType, ecenter, fr.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
1247 | positionsArrayRef);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1246:66: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function ‘void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:111:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
111 | void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:41:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:41:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void broadcastStateWithoutDynamics(MPI_Comm, bool, bool, t_state*)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function ‘void calc_mu(int, int, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:52:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
52 | void calc_mu(int start,
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<VerletbufAtomtype>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
/usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<VerletbufAtomtype> getVerletBufferAtomtypes(const gmx_mtop_t&, bool)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function ‘_ZN3gmx11Constraints4Impl5applyEbbxidNS_19ArrayRefWithPaddingINS_11BasicVectorIdEEEES5_NS_8ArrayRefIS4_EEPA3_KddPdS5_bPA3_dNS_18ConstraintVariableE._omp_fn.1’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:575:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
575 | settle_proj(*settled, econq, end_th - start_th,
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
576 | settle.iatoms.data() + start_th * (1 + NRAL(F_SETTLE)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
577 | pbc_null, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
578 | min_proj, calcvir_atom_end,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
579 | th == 0 ? constraintsVirial : threadConstraintsVirial[th]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:575:40: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:575:40: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function ‘int gmx::countFlexibleConstraints(gmx::ArrayRef<const InteractionList>, gmx::ArrayRef<const t_iparams>)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:869:5: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
869 | int countFlexibleConstraints(ArrayRef<const InteractionList> ilist, ArrayRef<const t_iparams> iparams)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In member function ‘bool gmx::Constraints::Impl::apply(bool, bool, int64_t, int, real, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3], real, real*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, bool, real (*)[3], gmx::ConstraintVariable)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:363:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
363 | bool Constraints::Impl::apply(bool bLog,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:464:30: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
464 | dd_move_x_constraints(cr->dd, box, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
465 | econq == ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:479:30: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
479 | bOK = constrain_lincs(bLog || bEner, ir, step, lincsd, inverseMasses_, cr, ms, x, xprime,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
480 | min_proj, box, pbc_null, hasMassPerturbedAtoms_, lambda, dvdlambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
481 | invdt, v.unpaddedArrayRef(), computeVirial, constraintsVirial, econq,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
482 | nrnb, maxwarn, &warncount_lincs);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:479:30: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:496:30: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
496 | bOK = constrain_shake(log, shaked.get(), inverseMasses_, *idef, ir, x.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
497 | xprime.unpaddedArrayRef(), min_proj, pbc_null, nrnb, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
498 | dvdlambda, invdt, v.unpaddedArrayRef(), computeVirial,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
499 | constraintsVirial, maxwarn < INT_MAX, econq);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:496:30: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:496:30: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:496:30: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function ‘void gmx::constr_recur(const gmx::ListOfLists<int>&, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, gmx::ArrayRef<int>, real, real, real*, int*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
60 | static void constr_recur(const ListOfLists<int>& at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In member function ‘bool gmx::Constraints::apply(bool, bool, int64_t, int, real, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3], real, real*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, bool, real (*)[3], gmx::ConstraintVariable)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:342:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
342 | bool Constraints::apply(bool bLog,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:358:24: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
358 | return impl_->apply(bLog, bEner, step, delta_step, step_scaling, std::move(x),
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
359 | std::move(xprime), min_proj, box, lambda, dvdlambda, std::move(v),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
360 | computeVirial, constraintsVirial, econq);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function ‘void gmx::constrain_velocities(gmx::Constraints*, bool, bool, int64_t, t_state*, real*, gmx_bool, real (*)[3])’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1277:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1277 | constr->apply(do_log, do_ene, step, 1, 1.0, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1278 | state->v.arrayRefWithPadding(), state->v.arrayRefWithPadding().unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1279 | state->box, state->lambda[efptBONDED], dvdlambda, ArrayRefWithPadding<RVec>(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1280 | computeVirial, constraintsVirial, ConstraintVariable::Velocities);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function ‘void gmx::constrain_coordinates(gmx::Constraints*, bool, bool, int64_t, t_state*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real*, gmx_bool, real (*)[3])’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1296:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1296 | constr->apply(do_log, do_ene, step, 1, 1.0, state->x.arrayRefWithPadding(), std::move(xp),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1297 | ArrayRef<RVec>(), state->box, state->lambda[efptBONDED], dvdlambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1298 | state->v.arrayRefWithPadding(), computeVirial, constraintsVirial,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1299 | ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function ‘void gmx::constr_recur(const gmx::ListOfLists<int>&, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, gmx::ArrayRef<int>, real, real, real*, int*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function ‘gmx::ListOfLists<int> gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:860:18: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
860 | ListOfLists<int> make_at2con(const gmx_moltype_t& moltype,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function ‘gmx::ListOfLists<int> gmx::make_at2con(int, gmx::ArrayRef<const InteractionList>, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:852:18: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
852 | ListOfLists<int> make_at2con(int numAtoms,
| ^~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::do_constrain_first(FILE*, gmx::Constraints*, const t_inputrec*, int, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, const real (*)[3], real)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1218:18: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1218 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, x, x, {}, box, lambda, &dvdl_dum, {},
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1219 | computeVirial, nullptr, gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1224:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1224 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, x, v, v.unpaddedArrayRef(), box, lambda,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1225 | &dvdl_dum, {}, computeVirial, nullptr, gmx::ConstraintVariable::Velocities);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:1251:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1251 | constr->apply(needsLogging, computeEnergy, step, -1, 1.0, x, savex.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1252 | {}, box, lambda, &dvdl_dum, v, computeVirial, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1253 | gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function ‘void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const std::vector<bool>&, gmx::ArrayRef<const double>)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:1268:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1268 | void andersen_tcoupl(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:1268:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function ‘gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx::Update*, const gmx::Constraints*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:293:17: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
293 | extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:321:24: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
321 | andersen_tcoupl(ir, step, cr, md, v, rate, upd->getAndersenRandomizeGroup(),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
322 | upd->getBoltzmanFactor());
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:321:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp: In function ‘void add_ebin_indexed(t_ebin*, int, gmx::ArrayRef<bool>, gmx::ArrayRef<const double>, gmx_bool)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp:199:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
199 | void add_ebin_indexed(t_ebin* eb,
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energydrifttracker.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function ‘void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], real (*)[3], t_state*, t_nrnb*, gmx::BoxDeformation*, bool)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:289:30: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
289 | boxDeformation->apply(localX, state->box, step);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor ‘DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:108:1: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
108 | DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor ‘DispersionCorrection::DispersionCorrection(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>, const interaction_const_t&, const char*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:518:1: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
518 | DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:528:5: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
528 | topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In member function ‘void ForeignLambdaTerms::finalizePotentialContributions(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, const t_lambda&)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:173:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
173 | void ForeignLambdaTerms::finalizePotentialContributions(gmx::ArrayRef<const double> dvdlLinear,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:173:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function ‘void accumulatePotentialEnergies(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:219:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
219 | void accumulatePotentialEnergies(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda* fepvals)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:235:65: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
235 | enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda, *fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:235:65: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:235:65: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In member function ‘void ForeignLambdaTerms::finalizeKineticContributions(gmx::ArrayRef<const double>, double, gmx::ArrayRef<const double>, const t_lambda&)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:245:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
245 | void ForeignLambdaTerms::finalizeKineticContributions(gmx::ArrayRef<const real> energyTerms,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:245:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function ‘void accumulateKineticLambdaComponents(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda&)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:280:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
280 | void accumulateKineticLambdaComponents(gmx_enerdata_t* enerd,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:296:59: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
296 | enerd->foreignLambdaTerms.finalizeKineticContributions(enerd->term, enerd->dvdl_lin[efptMASS],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | lambda, fepvals);
| ~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:296:59: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:296:59: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function ‘void calculateLongRangeNonbondeds(t_forcerec*, const t_inputrec*, const t_commrec*, t_nrnb*, gmx_wallcycle_t, const t_mdatoms*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ForceWithVirial*, gmx_enerdata_t*, const real (*)[3], const real*, const real (*)[3], const gmx::StepWorkload&, const DDBalanceRegionHandler&)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:101:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
101 | void calculateLongRangeNonbondeds(t_forcerec* fr,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:197:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
197 | status = gmx_pme_do(
| ~~~~~~~~~~^
198 | fr->pmedata,
| ~~~~~~~~~~~~
199 | gmx::constArrayRefFromArray(coordinates.data(), md->homenr - fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | forceWithVirial->force_, md->chargeA, md->chargeB, md->sqrt_c6A,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
202 | DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
203 | DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
204 | ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
205 | lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
206 | &ewaldOutput.dvdl[efptVDW], stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:197:40: note: parameter passing for argument of type ‘const gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:197:40: note: parameter passing for argument of type ‘const gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:226:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
226 | gmx_pme_calc_energy(
| ~~~~~~~~~~~~~~~~~~~^
227 | fr->pmedata, coordinates.subArray(md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
228 | gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | &Vlr_q);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:226:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:226:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/freeenergyparameters.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp: In member function ‘void gmx::EnergyOutput::addDataAtEnergyStep(bool, bool, double, real, const gmx_enerdata_t*, const t_lambda*, const t_expanded*, const real (*)[3], gmx::PTCouplingArrays, int, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const gmx_ekindata_t*, const real*, const gmx::Constraints*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp:891:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
891 | add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gpuforcereduction_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
In file included from /usr/include/c++/11/memory:76,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:49:
/usr/include/c++/11/bits/unique_ptr.h: In function ‘void init_forcerec(FILE*, const gmx::MDLogger&, t_forcerec*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, real (*)[3], const char*, const char*, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, real)’:
/usr/include/c++/11/bits/unique_ptr.h:962:30: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function ‘void gmx::lincs_update_atoms(gmx::Lincs*, int, real, gmx::ArrayRef<const double>, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*, real (*)[3])’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
445 | static void lincs_update_atoms(Lincs* li,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function ‘_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsEPKdPK9t_commrecPK14gmx_multisim_tNS_19ArrayRefWithPaddingIKNS_11BasicVectorIdEEEENSD_ISF_EENS_8ArrayRefISF_EEPA3_S5_P5t_pbcbdPddSK_bPA3_dNS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.1’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:711:23: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
711 | lincs_update_atoms(lincsd, th, 1.0, sol, r, (econq != ConstraintVariable::Force) ? invmass : nullptr,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
712 | as_rvec_array(fp.data()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:711:23: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp: In function ‘void compute_globals(gmx_global_stat*, t_commrec*, const t_inputrec*, t_forcerec*, gmx_ekindata_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3], const t_mdatoms*, t_nrnb*, t_vcm*, gmx_wallcycle_t, gmx_enerdata_t*, real (*)[3], real (*)[3], real (*)[3], real (*)[3], gmx::Constraints*, gmx::SimulationSignaller*, const real (*)[3], int*, gmx_bool*, int)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:297:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
297 | void compute_globals(gmx_global_stat* gstat,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:297:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:366:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
366 | calc_vcm_grp(*mdatoms, x, v, vcm);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:366:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:366:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function ‘_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsEPKdPK9t_commrecPK14gmx_multisim_tNS_19ArrayRefWithPaddingIKNS_11BasicVectorIdEEEENSD_ISF_EENS_8ArrayRefISF_EEPA3_S5_P5t_pbcbdPddSK_bPA3_dNS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.0’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1086:23: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1086 | lincs_update_atoms(lincsd, th, 1.0, mlambda, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1107:42: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1107 | dd_move_x_constraints(cr->dd, box, xpPadded.unpaddedArrayRef(), ArrayRef<RVec>(), FALSE);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1148:27: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1148 | lincs_update_atoms(lincsd, th, 1.0, blc_sol, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1155:27: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1155 | lincs_update_atoms(lincsd, th, invdt, mlambda, r, invmass, v);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function ‘bool gmx::constrain_lincs(bool, const t_inputrec&, int64_t, gmx::Lincs*, const real*, const t_commrec*, const gmx_multisim_t*, gmx::ArrayRefWithPadding<const gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3], t_pbc*, bool, real, real*, real, gmx::ArrayRef<gmx::BasicVector<double> >, bool, real (*)[3], gmx::ConstraintVariable, t_nrnb*, int, int*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:2259:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
2259 | bool constrain_lincs(bool computeRmsd,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:2259:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:40:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::MDAtoms::resizeChargeA(int)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::MDAtoms::resizeChargeB(int)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function ‘void gmx::set_lincs(const InteractionDefinitions&, int, const real*, real, bool, const t_commrec*, gmx::Lincs*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1911:94: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
1911 | make_at2con(natoms, idef.il, idef.iparams, flexibleConstraintTreatment(bDynamics));
| ^
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:47:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function ‘void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, int, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::WriteCheckpointDataHolder*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:513:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
513 | void mdoutf_write_to_trajectory_files(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:539:31: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
539 | dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
540 | state_local->cg_gl, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:539:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:545:31: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
545 | dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
546 | state_local->cg_gl, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:545:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:552:27: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
552 | dd_collect_vec(
| ~~~~~~~~~~~~~~^
553 | cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl, f_local,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(of->f_global), f_local.size()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:552:27: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function ‘int add_binr(t_bin*, gmx::ArrayRef<const double>)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
103 | int add_binr(t_bin* b, gmx::ArrayRef<const real> r)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function ‘void extract_binr(t_bin*, int, gmx::ArrayRef<double>)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
160 | void extract_binr(t_bin* b, int index, gmx::ArrayRef<real> r)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp: In function ‘void gmx::cshake(const int*, int, int*, int, gmx::ArrayRef<const double>, gmx::ArrayRef<gmx::BasicVector<double> >, const t_pbc*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real, const real*, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
270 | void cshake(const int iatom[],
| ^~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:270:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp: In function ‘void gmx::settle_proj(const gmx::SettleData&, gmx::ConstraintVariable, int, const t_iatom*, const t_pbc*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, int, real (*)[3])’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp:260:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
260 | void settle_proj(const SettleData& settled,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp:260:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp:260:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp: In function ‘bool gmx::bshakef(FILE*, gmx::shakedata*, const real*, const InteractionDefinitions&, const t_inputrec&, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const t_pbc*, t_nrnb*, real, real*, real, gmx::ArrayRef<gmx::BasicVector<double> >, bool, real (*)[3], bool, gmx::ConstraintVariable)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:655:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
655 | static bool bshakef(FILE* log,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:655:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:655:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
505 | cshake(iatom, ncon, &nit, maxnit, constraint_distance_squared, prime, pbc, rij,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
506 | half_of_reduced_mass, omega, invmass, distance_squared_tolerance,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
507 | scaled_lagrange_multiplier, &error);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:505:19: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp: In function ‘bool gmx::constrain_shake(FILE*, gmx::shakedata*, const real*, const InteractionDefinitions&, const t_inputrec&, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const t_pbc*, t_nrnb*, real, real*, real, gmx::ArrayRef<gmx::BasicVector<double> >, bool, real (*)[3], bool, gmx::ConstraintVariable)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:761:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
761 | bool constrain_shake(FILE* log,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:761:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:761:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:761:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:788:26: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
788 | bOK = bshakef(log, shaked, invmass, idef, ir, x_s, xprime, pbc, nrnb, lambda, dvdlambda,
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
789 | invdt, v, bCalcVir, vir_r_m_dr, bDumpOnError, econq);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:788:26: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:788:26: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:792:26: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
792 | bOK = bshakef(log, shaked, invmass, idef, ir, x_s, vprime, pbc, nrnb, lambda, dvdlambda,
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
793 | invdt, {}, bCalcVir, vir_r_m_dr, bDumpOnError, econq);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:792:26: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp:792:26: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function ‘void postProcessForceWithShiftForces(t_nrnb*, gmx_wallcycle_t, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ForceOutputs*, real (*)[3], const t_mdatoms&, const t_forcerec&, gmx::VirtualSitesHandler*, const gmx::StepWorkload&)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:282:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
282 | static void postProcessForceWithShiftForces(t_nrnb* nrnb,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:307:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
307 | vsite->spreadForces(x, f, virialHandling, fshift, nullptr, nrnb, box, wcycle);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:307:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:307:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:307:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function ‘void postProcessForces(const t_commrec*, int64_t, t_nrnb*, gmx_wallcycle_t, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ForceOutputs*, real (*)[3], const t_mdatoms*, const t_forcerec*, gmx::VirtualSitesHandler*, const gmx::StepWorkload&)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:320:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
320 | static void postProcessForces(const t_commrec* cr,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:357:32: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
357 | vsite->spreadForces(x, forceWithVirial.force_, virialHandling, {}, virial, nrnb, box, wcycle);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:357:32: note: parameter passing for argument of type ‘const gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:357:32: note: parameter passing for argument of type ‘const gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:357:32: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function ‘void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ForceBuffersView*, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, gmx::ArrayRef<const double>, t_forcerec*, gmx::MdrunScheduleWorkload*, gmx::VirtualSitesHandler*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1125:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1125 | void do_force(FILE* fplog,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1236:41: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1236 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1279:43: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1279 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1306:62: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1306 | fr->wholeMoleculeTransform->updateForAtomPbcJumps(x.unpaddedArrayRef(), box);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1325:30: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1325 | nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1326 | fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1332:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1332 | nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1336:31: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1336 | nbv->setAtomProperties(gmx::constArrayRefFromArray(mdatoms->typeA, mdatoms->nr),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1337 | gmx::constArrayRefFromArray(mdatoms->chargeA, mdatoms->nr), fr->cginfo);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1336:31: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1409:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1409 | nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1409:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1487:53: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1487 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1505:51: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1505 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1513:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1513 | nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1513:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1674:38: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1674 | nbv->dispatchFreeEnergyKernel(InteractionLocality::Local, fr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1675 | as_rvec_array(x.unpaddedArrayRef().data()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1676 | &forceOutNonbonded->forceWithShiftForces(), *mdatoms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1677 | inputrec->fepvals, lambda, enerd, stepWork, nrnb);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1681:42: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1681 | nbv->dispatchFreeEnergyKernel(InteractionLocality::NonLocal, fr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1682 | as_rvec_array(x.unpaddedArrayRef().data()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1683 | &forceOutNonbonded->forceWithShiftForces(), *mdatoms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1684 | inputrec->fepvals, lambda, enerd, stepWork, nrnb);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1713:53: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1713 | nbnxn_atomdata_add_nbat_fshift_to_fshift(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
1714 | *nbv->nbat, forceOutNonbonded->forceWithShiftForces().shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1732:35: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1732 | real dvdl_walls = do_walls(*inputrec, *fr, box, *mdatoms, x.unpaddedConstArrayRef(),
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | &forceOutMtsLevel0.forceWithVirial(), lambda[efptVDW],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | enerd->grpp.ener[egLJSR].data(), nrnb);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1764:35: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1764 | listedForces.calculate(
| ~~~~~~~~~~~~~~~~~~~~~~^
1765 | wcycle, box, inputrec->fepvals, cr, ms, x, xWholeMolecules, fr->fcdata.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1766 | hist, &forceOut, fr, &pbc, enerd, nrnb, lambda.data(), mdatoms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1767 | DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1773:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1773 | calculateLongRangeNonbondeds(fr, inputrec, cr, nrnb, wcycle, mdatoms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1774 | x.unpaddedConstArrayRef(), &forceOutMtsLevel1->forceWithVirial(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1775 | enerd, box, lambda.data(), as_rvec_array(dipoleData.muStateAB),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1776 | stepWork, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:645:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
645 | enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
646 | *inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:645:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:645:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
651 | enerd->term[F_COM_PULL] += awh->applyBiasForcesAndUpdateBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
652 | inputrec->pbcType, mdatoms->massT, foreignLambdaDeltaH, foreignLambdaDhDl, box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
653 | forceWithVirial, t, step, wcycle, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:651:73: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1845:46: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1845 | stateGpu->copyForcesToGpu(forceOutMtsLevel0.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1846 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1855:48: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1855 | stateGpu->copyForcesFromGpu(forceOutMtsLevel0.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1856 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1866:57: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1866 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat, forceWithShiftForces.shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1901:46: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1901 | stateGpu->copyForcesToGpu(forceOutMtsLevel0.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1902 | AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2032:42: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2032 | stateGpu->copyForcesToGpu(forceWithShift, locality);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2049:44: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
2049 | stateGpu->copyForcesFromGpu(forceWithShift, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2072:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2072 | postProcessForceWithShiftForces(nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutMtsLevel0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2073 | vir_force, *mdatoms, *fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2072:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2077:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2077 | postProcessForceWithShiftForces(nrnb, wcycle, box, x.unpaddedArrayRef(), forceOutMtsLevel1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2078 | vir_force, *mdatoms, *fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2077:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2100:26: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2100 | postProcessForces(cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutCombined,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2101 | vir_force, mdatoms, fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2105:30: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2105 | postProcessForces(cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), forceOutMtsLevel1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2106 | vir_force, mdatoms, fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2116:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
2116 | accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2100:26: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2100 | postProcessForces(cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutCombined,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2101 | vir_force, mdatoms, fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2072:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2072 | postProcessForceWithShiftForces(nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutMtsLevel0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2073 | vir_force, *mdatoms, *fr, vsite, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2072:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp: In member function ‘void gmx::UpdateConstrainGpu::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_gpu_impl.cpp:73:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_grp_tcstat>’ changed in GCC 7.1
73 | void UpdateConstrainGpu::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function ‘void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, const gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, const gmx::EnergyOutput&, gmx_ekindata_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:58:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
58 | void do_md_trajectory_writing(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:149:41: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
149 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
150 | state_global, observablesHistory, f, &checkpointDataHolder);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In member function ‘void gmx::Update::Impl::update_sd_second_half(const t_inputrec&, int64_t, real*, const t_mdatoms*, t_state*, const t_commrec*, t_nrnb*, gmx_wallcycle_t, gmx::Constraints*, bool, bool)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1403:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1403 | constr->apply(do_log, do_ene, step, 1, 0.5, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1404 | xp_.arrayRefWithPadding(), ArrayRef<RVec>(), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1405 | state->lambda[efptBONDED], dvdlambda, state->v.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1406 | computeVirial, nullptr, ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function ‘void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:80:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
80 | void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp: In function ‘gmx::RangePartitioning gmx::makeUpdateGroups(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp:340:26: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
340 | static RangePartitioning makeUpdateGroups(const gmx_moltype_t& moltype, gmx::ArrayRef<const t_iparams> iparams)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp:359:85: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
359 | FlexibleConstraintTreatment::Include);
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp: In function ‘void calc_vcm_grp(const t_mdatoms&, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const gmx::BasicVector<double> >, t_vcm*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp:155:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
155 | void calc_vcm_grp(const t_mdatoms& md,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp:155:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp: In function ‘void process_and_stopcm_grp(FILE*, t_vcm*, const t_mdatoms&, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp:579:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
579 | void process_and_stopcm_grp(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp:579:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:40:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::Update::setNumAtoms(int)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘gmx::Update::Impl::Impl(const t_inputrec&, gmx::BoxDeformation*)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function ‘void gmx::construct_vsites_thread(gmx::ArrayRef<gmx::BasicVector<double> >, real, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>, const t_pbc*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:625:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
625 | static void construct_vsites_thread(ArrayRef<RVec> x,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:625:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:625:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp: In member function ‘void gmx::WholeMoleculeTransform::updateForAtomPbcJumps(gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3])’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp:57:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
57 | void WholeMoleculeTransform::updateForAtomPbcJumps(ArrayRef<const RVec> x, const matrix box)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp: In member function ‘gmx::ArrayRef<const gmx::BasicVector<double> > gmx::WholeMoleculeTransform::wholeMoleculeCoordinates(gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3])’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wholemoleculetransform.cpp:62:22: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
62 | ArrayRef<const RVec> WholeMoleculeTransform::wholeMoleculeCoordinates(ArrayRef<const RVec> x, const matrix box)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function ‘void gmx::construct_vsites(const gmx::ThreadingInfo*, gmx::ArrayRef<gmx::BasicVector<double> >, real, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>, const gmx::DomainInfo&, const real (*)[3])’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:769:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
769 | static void construct_vsites(const ThreadingInfo* threadingInfo,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:769:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:769:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:809:32: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
809 | construct_vsites_thread(x, dt, v, ip, ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:835:32: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
835 | construct_vsites_thread(x, dt, v, ip, threadingInfo->threadDataNonLocalDependent().ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function ‘_ZN3gmxL16construct_vsitesEPKNS_13ThreadingInfoENS_8ArrayRefINS_11BasicVectorIdEEEEdS6_NS3_IK9t_iparamsEENS3_IK15InteractionListEERKNS_10DomainInfoEPA3_Kd._omp_fn.0’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:822:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
822 | construct_vsites_thread(x, dt, v, ip, tData.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:829:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
829 | construct_vsites_thread(x, dt, v, ip, tData.idTask.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp: In function ‘real do_walls(const t_inputrec&, const t_forcerec&, const real (*)[3], const t_mdatoms&, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ForceWithVirial*, real, real*, t_nrnb*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp:162:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
162 | real do_walls(const t_inputrec& ir,
| ^~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function ‘void gmx::spreadForceForThread(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>, const t_pbc*) [with gmx::VirtualSitesHandler::VirialHandling virialHandling = gmx::VirtualSitesHandler::VirialHandling::NonLinear]’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1728:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1728 | static void spreadForceForThread(ArrayRef<const RVec> x,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1728:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1728:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1728:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function ‘void gmx::spreadForceWrapper(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::VirialHandling, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], bool, gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>, const t_pbc*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1823:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1823 | static void spreadForceWrapper(ArrayRef<const RVec> x,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1823:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1823:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1823:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1847:60: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1847 | spreadForceForThread<VirialHandling::NonLinear>(x, f, fshift, dxdf, ip, ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1847:60: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function ‘_ZN3gmx19VirtualSitesHandler4Impl12spreadForcesENS_8ArrayRefIKNS_11BasicVectorIdEEEENS2_IS4_EENS0_14VirialHandlingES7_PA3_dP6t_nrnbPA3_KdP13gmx_wallcycle._omp_fn.0’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2006:35: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
2006 | spreadForceWrapper(x, f, virialHandling, fshift_t, tData.dxdf, false, iparams_,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2007 | tData.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2006:35: note: parameter passing for argument of type ‘const gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1969:39: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1969 | spreadForceWrapper(x, idTask->force, virialHandling, fshift_t, tData.dxdf, true,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1970 | iparams_, tData.idTask.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1969:39: note: parameter passing for argument of type ‘const gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function ‘void gmx::VirtualSitesHandler::Impl::construct(gmx::ArrayRef<gmx::BasicVector<double> >, real, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3]) const’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:839:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
839 | void VirtualSitesHandler::Impl::construct(ArrayRef<RVec> x, real dt, ArrayRef<RVec> v, const matrix box) const
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:839:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:841:21: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
841 | construct_vsites(&threadingInfo_, x, dt, v, iparams_, ilists_, domainInfo_, box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:841:21: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:841:21: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:841:21: note: parameter passing for argument of type ‘const gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function ‘void gmx::VirtualSitesHandler::construct(gmx::ArrayRef<gmx::BasicVector<double> >, real, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3]) const’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:844:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
844 | void VirtualSitesHandler::construct(ArrayRef<RVec> x, real dt, ArrayRef<RVec> v, const matrix box) const
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:844:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:846:21: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
846 | impl_->construct(x, dt, v, box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:846:21: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:846:21: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function ‘void gmx::constructVirtualSites(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<const t_iparams>, gmx::ArrayRef<const InteractionList>)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:849:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
849 | void constructVirtualSites(ArrayRef<RVec> x, ArrayRef<const t_iparams> ip, ArrayRef<const InteractionList> ilist)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:849:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:854:21: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
854 | construct_vsites(nullptr, x, 0, {}, ip, ilist, domainInfo, nullptr);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:854:21: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:854:21: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:854:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function ‘void gmx::constructVirtualSitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:917:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
917 | void constructVirtualSitesGlobal(const gmx_mtop_t& mtop, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function ‘void gmx::VirtualSitesHandler::Impl::spreadForces(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::VirtualSitesHandler::VirialHandling, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], t_nrnb*, const real (*)[3], gmx_wallcycle*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1868 | void VirtualSitesHandler::Impl::spreadForces(ArrayRef<const RVec> x,
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1868:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1898:26: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1898 | dd_clear_f_vsites(*domainInfo_.domdec_, f);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1906:27: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1906 | spreadForceWrapper(x, f, virialHandling, fshift, dxdf, true, iparams_, ilists_, pbc_null);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1906:27: note: parameter passing for argument of type ‘const gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1923:27: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1923 | spreadForceWrapper(x, f, virialHandling, fshift, nlDependentVSites.dxdf, true, iparams_,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1924 | nlDependentVSites.ilist, pbc_null);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:1923:27: note: parameter passing for argument of type ‘const gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2043:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
2043 | dd_move_f_vsites(*domainInfo_.domdec_, f, fshift);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2043:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2043:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function ‘void gmx::VirtualSitesHandler::spreadForces(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::VirtualSitesHandler::VirialHandling, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], t_nrnb*, const real (*)[3], gmx_wallcycle*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2097:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2097 | void VirtualSitesHandler::spreadForces(ArrayRef<const RVec> x,
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2097:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2097:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2106:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
2106 | impl_->spreadForces(x, f, virialHandling, fshift, virial, nrnb, box, wcycle);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2106:24: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2106:24: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2106:24: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp: In member function ‘void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:396:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
396 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:396:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:418:45: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
418 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
419 | forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:418:45: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationgrid.h:105:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
105 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function ‘void gmx::ThreadingInfo::setVirtualSites(gmx::ArrayRef<const InteractionList>, gmx::ArrayRef<const t_iparams>, const t_mdatoms&, bool)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2425:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
2425 | void ThreadingInfo::setVirtualSites(ArrayRef<const InteractionList> ilists,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In member function ‘void gmx::VirtualSitesHandler::Impl::setVirtualSites(gmx::ArrayRef<const InteractionList>, const t_mdatoms&)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2688:35: note: parameter passing for argument of type ‘const gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
2688 | threadingInfo_.setVirtualSites(ilists, iparams_, mdatoms, domainInfo_.useDomdec());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:2688:35: note: parameter passing for argument of type ‘const gmx::ArrayRef<const t_iparams>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp: In member function ‘gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
105 | gmx::ArrayRef<const double> Bias::calcForceAndUpdateBias(const awh_dvec coordValue,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:105:29: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
146 | convolvedBias = state_.updateProbabilityWeightsAndConvolvedBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
147 | dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | &probWeightNeighbor);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
152 | updateForceCorrelationGrid(probWeightNeighbor, neighborLambdaDhdl, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:152:39: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:154:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
154 | state_.sampleCoordAndPmf(dimParams_, grid_, probWeightNeighbor, convolvedBias);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:154:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
168 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
170 | tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:168:34: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
180 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
181 | dimParams_, grid_, coordState.umbrellaGridpoint(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
182 | moveUmbrella ? neighborLambdaDhdl : ArrayRef<const double>{}, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:180:57: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
192 | state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
193 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:192:40: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
146 | convolvedBias = state_.updateProbabilityWeightsAndConvolvedBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
147 | dimParams_, grid_, moveUmbrella ? neighborLambdaEnergies : ArrayRef<const double>{},
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | &probWeightNeighbor);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.cpp:146:72: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasparams.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp: In member function ‘real gmx::Awh::applyBiasForcesAndUpdateBias(PbcType, const real*, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, const real (*)[3], gmx::ForceWithVirial*, double, int64_t, gmx_wallcycle*, FILE*)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:294:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
294 | real Awh::applyBiasForcesAndUpdateBias(PbcType pbcType,
| ^~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:294:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:350:85: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
350 | gmx::ArrayRef<const double> biasForce = biasCts.bias_.calcForceAndUpdateBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
351 | coordValue, neighborLambdaEnergies, neighborLambdaDhdl, &biasPotential,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
352 | &biasPotentialJump, commRecord_, multiSimRecord_, t, step, seed_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:350:85: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:350:85: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In function ‘_ZN3gmx13ThreadingInfo15setVirtualSitesENS_8ArrayRefIK15InteractionListEENS1_IK9t_iparamsEERK9t_mdatomsb._omp_fn.0’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.h:70,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/awh.cpp:48:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BiasCoupledToSystem>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/memory:63,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp:47:
/usr/include/c++/11/bits/stl_algobase.h: In function ‘_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >; _Predicate = __gnu_cxx::__ops::_Iter_pred<gmx::BiasGrid::hasLambdaAxis() const::<lambda(const auto:22&)> >]’:
/usr/include/c++/11/bits/stl_algobase.h:2061:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
2061 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~
/usr/include/c++/11/bits/stl_algobase.h:2061:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algobase.h: In function ‘bool gmx::pointsAlongLambdaAxis(const gmx::BiasGrid&, int, int)’:
/usr/include/c++/11/bits/stl_algobase.h:2114:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
2114 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2115 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In constructor ‘gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*, int, int)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algobase.h: In function ‘bool gmx::pointsHaveDifferentLambda(const gmx::BiasGrid&, int, int)’:
/usr/include/c++/11/bits/stl_algobase.h:2114:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
2114 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2115 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/dimparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:61,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::GridAxis>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, int, const int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::GridAxis>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In constructor ‘gmx::BiasGrid::BiasGrid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, int, int&, bool}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::GridAxis>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biaswriter.cpp
/usr/include/c++/11/bits/vector.tcc: In function ‘void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::BiasGrid&, const string&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In function ‘void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:351:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::PointState>’ changed in GCC 7.1
351 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, int, gmx::ArrayRef<const double>, gmx::ArrayRef<double>) const’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:475:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
475 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:475:8: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
508 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:508:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:529:38: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
529 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, neighborLambdaDhdl, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:529:38: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
539 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:539:8: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:549:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
549 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
550 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:549:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:553:69: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
553 | double newPotential = calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
554 | dimParams, grid, coordState_.umbrellaGridpoint(), neighborLambdaDhdl, newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:553:69: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘void gmx::BiasState::sampleProbabilityWeights(const gmx::BiasGrid&, gmx::ArrayRef<const double>)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1350:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1350 | void BiasState::sampleProbabilityWeights(const BiasGrid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘void gmx::BiasState::sampleCoordAndPmf(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, double)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1404:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1404 | void BiasState::sampleCoordAndPmf(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp: In member function ‘void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::BiasGrid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/coordstate.cpp:129:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const BiasGrid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationhistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘double gmx::BiasState::updateProbabilityWeightsAndConvolvedBias(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, gmx::ArrayRef<const double>, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >*) const’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1242:8: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1242 | double BiasState::updateProbabilityWeightsAndConvolvedBias(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp: In member function ‘void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/correlationtensor.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::CorrelationBlockData>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In constructor ‘gmx::CorrelationTensor::CorrelationTensor(int, int, double)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/pointstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp: In member function ‘void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::BiasGrid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
1159 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/read_params.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.cpp:1159:62: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function ‘double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
78 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function ‘double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
210 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:243:56: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
243 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/histogramsize.cpp:243:56: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual const std::vector<double>& gmx::{anonymous}::UnitAmplitudes::operator()(const t_mdatoms&, gmx::ArrayRef<const int>)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp: In member function ‘void gmx::DensityFittingForceProvider::Impl::calculateForces(const gmx::ForceProviderInput&, gmx::ForceProviderOutput*)’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp:276:33: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
276 | (*affineTransformation_)(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp:292:36: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
292 | transformationToDensityLattice_(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp:340:82: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
340 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(forces_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp:47:
/usr/include/c++/11/optional: In constructor ‘gmx::DensityFittingForceProvider::Impl::Impl(const gmx::DensityFittingParameters&, gmx::basic_mdspan<const float, gmx::extents<-1, -1, -1> >, const gmx::TranslateAndScale&, const gmx::LocalAtomSet&, PbcType, double, const gmx::DensityFittingForceProviderState&)’:
/usr/include/c++/11/optional:418:11: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >’ changed in GCC 7.1
418 | ::new
| ^~~~~
419 | (std::__addressof(static_cast<_Dp*>(this)->_M_payload._M_payload))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
420 | _Stored_type(std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp: In member function ‘void ListedForces::calculate(gmx_wallcycle*, const real (*)[3], const t_lambda*, const t_commrec*, const gmx_multisim_t*, gmx::ArrayRefWithPadding<const gmx::BasicVector<double> >, gmx::ArrayRef<const gmx::BasicVector<double> >, t_fcdata*, history_t*, gmx::ForceOutputs*, const t_forcerec*, const t_pbc*, gmx_enerdata_t*, t_nrnb*, const real*, const t_mdatoms*, int*, const gmx::StepWorkload&)’:
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp:698:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
698 | void ListedForces::calculate(struct gmx_wallcycle* wcycle,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp:760:55: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
760 | enerd->term[F_ORIRESDEV] = calc_orires_dev(
| ~~~~~~~~~~~~~~~^
761 | ms, idef.il[F_ORIRES].size(), idef.il[F_ORIRES].iatoms.data(), idef.iparams.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
762 | md, xWholeMolecules, x, fr->bMolPBC ? pbc : nullptr, fcdata->orires, hist);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp: In function ‘real calc_orires_dev(const gmx_multisim_t*, int, const t_iatom*, const t_iparams*, const t_mdatoms*, gmx::ArrayRef<const gmx::BasicVector<double> >, const real (*)[3], const t_pbc*, t_oriresdata*, history_t*)’:
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp:384:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
384 | real calc_orires_dev(const gmx_multisim_t* ms,
| ^~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<pme_setup_t>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function ‘void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)’:
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:555:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
555 | static void pme_load_balance(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function ‘void pme_loadbal_do(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, t_forcerec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_wallcycle_t, int64_t, int64_t, gmx_bool*, bool)’:
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:901:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
901 | void pme_loadbal_do(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:1040:25: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1040 | pme_load_balance(pme_lb, cr, fp_err, fp_log, mdlog, ir, box, x,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1041 | pme_lb->cycles_c - cycles_prev, fr->ic, fr->nbv.get(), &fr->pmedata, step);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function ‘void gmx_pme_calc_energy(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real*)’:
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:950:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
950 | void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:950:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:75:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:75:
/usr/include/c++/11/bits/stl_vector.h: In function ‘int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode, const gmx::DeviceStreamManager*)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:720:47: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
720 | stateGpu->copyCoordinatesToGpu(gmx::ArrayRef<gmx::RVec>(pme_pp->x), gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:737:23: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
737 | gmx_pme_do(pme, pme_pp->x, pme_pp->f, pme_pp->chargeA.data(), pme_pp->chargeB.data(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
738 | pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(), pme_pp->sigmaA.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
739 | pme_pp->sigmaB.data(), box, cr, maxshift_x, maxshift_y, mynrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
740 | output.coulombVirial_, output.lennardJonesVirial_, &output.coulombEnergy_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
741 | &output.lennardJonesEnergy_, lambda_q, lambda_lj, &dvdlambda_q,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
742 | &dvdlambda_lj, stepWork);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:737:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:737:23: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function ‘void dd_pmeredist_f(gmx_pme_t*, PmeAtomComm*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)’:
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:388:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
388 | void dd_pmeredist_f(struct gmx_pme_t* pme, PmeAtomComm* atc, gmx::ArrayRef<gmx::RVec> f, gmx_bool bAddF)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function ‘int gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real*, real*, real*, real*, real*, real*, const real (*)[3], const t_commrec*, int, int, t_nrnb*, gmx_wallcycle*, real (*)[3], real (*)[3], real*, real*, real, real, real*, real*, const gmx::StepWorkload&)’:
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1002:5: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1002 | int gmx_pme_do(struct gmx_pme_t* pme,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1002:5: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1151:33: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1151 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, coefficient);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1151:33: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1368:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1368 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, RedistC6);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1368:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1377:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1377 | do_redist_pos_coeffs(pme, cr, FALSE, coordinates, RedistSigma);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1377:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function ‘void do_redist_pos_coeffs(gmx_pme_t*, const t_commrec*, gmx_bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*)’:
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:453:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
453 | void do_redist_pos_coeffs(struct gmx_pme_t* pme,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/device_management.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/membedholder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp: In member function ‘void gmx::LegacySimulator::do_mimic()’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:227:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
227 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:300:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
300 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
301 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
302 | force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
303 | &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:300:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:305:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
305 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
306 | makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
307 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:392:33: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
392 | vsite->construct(state->x, ir->delta_t, state->v, state->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:392:33: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:392:33: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:424:32: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
424 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
425 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
426 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
427 | state->v.arrayRefWithPadding(), state->box, state->lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
428 | &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
429 | fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:440:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
440 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
441 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
442 | &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
443 | vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:453:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
453 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
454 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
455 | energyOutput, ekind, f.view().force(), isCheckpointingStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
456 | doRerun, isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:468:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
468 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
469 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
470 | enerd, nullptr, nullptr, nullptr, nullptr, constr, &signaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
471 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
472 | CGLO_GSTAT | CGLO_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~
473 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
474 | : 0));
| ~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:468:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:475:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
475 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
476 | &top, makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:487:31: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
487 | dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
488 | flocal, ftemp);
| ~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:487:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:512:46: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
512 | accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function ‘void gmx::LegacySimulator::do_md()’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:257:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
257 | initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:515:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
515 | vsite->construct(state->x, ir->delta_t, {}, state->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:515:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:515:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:586:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
586 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
587 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
588 | enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
589 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
590 | cglo_flags_iteration
| ~~~~~~~~~~~~~~~~~~~~
591 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
592 | : 0));
| ~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:586:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:600:35: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
600 | process_and_stopcm_grp(fplog, &vcm, *mdatoms, x, makeArrayRef(state->v));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:600:35: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:600:35: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:604:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
604 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
605 | makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
606 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:615:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
615 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
616 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
617 | enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
618 | state->box, nullptr, &bSumEkinhOld, cglo_flags & ~CGLO_PRESSURE);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:615:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:737:49: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
737 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:741:27: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
741 | pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
742 | fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
743 | &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:798:44: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
798 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:803:45: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
803 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:865:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
865 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
866 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
867 | enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
868 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
869 | CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:865:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:870:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
870 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
871 | &top, makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
872 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:918:32: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
918 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
919 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
920 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
921 | state->v.arrayRefWithPadding(), state->box, state->lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
922 | &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
923 | fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:945:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
945 | do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
946 | nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
947 | &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
948 | vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
949 | (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1007:32: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1007 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1008 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1009 | enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1010 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1011 | (bGStat ? CGLO_GSTAT : 0) | (bCalcEner ? CGLO_ENERGY : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1012 | | (bTemp ? CGLO_TEMPERATURE : 0) | (bPres ? CGLO_PRESSURE : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1013 | | (bPres ? CGLO_CONSTRAINT : 0) | (bStopCM ? CGLO_STOPCM : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1014 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1015 | : 0)
| ~~~~
1016 | | CGLO_SCALEEKIN);
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1007:32: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1024:48: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1024 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1025 | top_global, &top, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1026 | state->box, &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1029:43: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1029 | process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1030 | makeArrayRef(state->v));
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1029:43: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1029:43: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1068:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1068 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1069 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1070 | enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1071 | state->box, nullptr, &bSumEkinhOld, CGLO_GSTAT | CGLO_TEMPERATURE);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1068:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1099:50: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1099 | accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1127:45: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1127 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1135:44: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1135 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1151:40: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1151 | stateGpu->copyForcesFromGpu(f.view().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1158:33: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1158 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1159 | observablesHistory, top_global, fr, outf, energyOutput, ekind,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | f.view().force(), checkpointHandler->isCheckpointingStep(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1161 | bRerunMD, bLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1193:55: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1193 | bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1268:46: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1268 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1269:47: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1269 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1276:42: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1276 | stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1282:42: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1282 | stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1289:34: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_grp_tcstat>’ changed in GCC 7.1
1289 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1290 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1291 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1292 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1299:48: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1299 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1345:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1345 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1346 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1347 | force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, lastbox,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1348 | nullptr, &bSumEkinhOld, (bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1345:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1391:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1391 | vsite->construct(state->x, ir->delta_t, state->v, state->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1391:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1391:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1410:53: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1410 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1423:32: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1423 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1424 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1425 | wcycle, enerd, force_vir, shake_vir, total_vir, pres, constr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1426 | &signaller, lastbox, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1427 | (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1428 | | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1429 | | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1430 | | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1431 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1432 | : 0));
| ~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1423:32: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1433:48: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1433 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1434 | top_global, &top, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1435 | state->box, &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1438:43: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1438 | process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1439 | makeArrayRef(state->v));
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1438:43: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1438:43: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1445:55: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1445 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1453:58: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1453 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1471:46: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1471 | accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1572:38: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
1572 | printLambdaStateToLog(fplog, state->lambda, isInitialOutput);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function ‘void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:834:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
834 | vsite->construct(ems->s.x, 1, {}, ems->s.box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:834:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:834:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:848:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
848 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
849 | top, ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist, &ems->f.view(), force_vir,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 | mdAtoms->mdatoms(), enerd, ems->s.lambda, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
851 | GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
852 | | (bNS ? GMX_FORCE_NS : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
853 | DDBalanceRegionHandler(cr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:896:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
896 | constr->apply(needsLogging, computeEnergy, count, 0, 1.0, ems->s.x.arrayRefWithPadding(), f,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
897 | f.unpaddedArrayRef(), ems->s.box, ems->s.lambda[efptBONDED], &dvdl_constr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
898 | gmx::ArrayRefWithPadding<RVec>(), computeVirial, shake_vir,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
899 | gmx::ConstraintVariable::ForceDispl);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:913:42: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
913 | accumulateKineticLambdaComponents(enerd, ems->s.lambda, *inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function ‘void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, const gmx_mtop_t*, em_state_t*, gmx_localtop_t*, t_nrnb*, t_forcerec*, gmx::MDAtoms*, gmx_global_stat**, gmx::VirtualSitesHandler*, gmx::Constraints*, gmx_shellfc_t**)’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:397:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
397 | initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:461:26: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
461 | constr->apply(needsLogging, computeEnergy, -1, 0, 1.0, ems->s.x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
462 | ems->s.x.arrayRefWithPadding(), ArrayRef<RVec>(), ems->s.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
463 | ems->s.lambda[efptFEP], &dvdl_constr, gmx::ArrayRefWithPadding<RVec>(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
464 | computeVirial, nullptr, gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function ‘void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, const gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:539:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
539 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
540 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
541 | observablesHistory, state->f.view().force(), &checkpointDataHolder);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:31: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
551 | dd_collect_vec(cr->dd, state->s.ddp_count, state->s.ddp_count_cg_gl, state->s.cg_gl,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | state->s.x, globalXRef);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:31: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function ‘void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, const gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:539:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
539 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
540 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
541 | observablesHistory, state->f.view().force(), &checkpointDataHolder);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function ‘void gmx::LegacySimulator::do_lbfgs()’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1765:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1765 | vsite->construct(state_global->x, 1, {}, state_global->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1765:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1765:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1867:41: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
1867 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1868 | static_cast<real>(step), &ems.s, state_global, observablesHistory,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1869 | ems.f.view().force(), &checkpointDataHolder);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp: In member function ‘void gmx::LegacySimulator::do_rerun()’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:285:23: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
285 | initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:354:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
354 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
355 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
356 | force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
357 | &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:354:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:359:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
359 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
360 | makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
361 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:165:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
165 | vsite->construct(globalState->x, timeStep, globalState->v, globalState->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:165:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:165:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:540:32: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
540 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
541 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
542 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
543 | state->v.arrayRefWithPadding(), state->box, state->lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
544 | &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
545 | fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:556:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
556 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
557 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
558 | &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
559 | vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:569:37: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
569 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
570 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
571 | energyOutput, ekind, f.view().force(), isCheckpointingStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
572 | doRerun, isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:580:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
580 | vsite->construct(state->x, ir->delta_t, state->v, state->box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:580:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:580:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:591:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
591 | compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
592 | makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
593 | enerd, force_vir, shake_vir, total_vir, pres, constr, &signaller,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
594 | state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
595 | CGLO_GSTAT | CGLO_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~
596 | | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
597 | : 0));
| ~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:591:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:598:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
598 | checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
599 | &top, makeConstArrayRef(state->x), state->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
600 | &shouldCheckNumberOfBondedInteractions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function ‘void gmx::LegacySimulator::do_nm()’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:2774:40: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
2774 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, nullptr, step, inputrec,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2775 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2776 | state_work.s.natoms, state_work.s.x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2777 | state_work.s.v.arrayRefWithPadding(), state_work.s.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2778 | state_work.s.lambda, &state_work.s.hist, &state_work.f.view(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2779 | vir, mdatoms, nrnb, wcycle, shellfc, fr, runScheduleWork, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2780 | mu_tot, vsite, DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function ‘bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, gmx::ArrayRefWithPadding<const gmx::BasicVector<double> >, em_state_t*, gmx::Constraints*, int64_t)’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:689:36: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
689 | validStep = constr->apply(
| ~~~~~~~~~~~~~^
690 | TRUE, TRUE, count, 0, 1.0, s1->x.arrayRefWithPadding(), s2->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
691 | ArrayRef<RVec>(), s2->box, s2->lambda[efptBONDED], &dvdl_constr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
692 | gmx::ArrayRefWithPadding<RVec>(), false, nullptr, gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationinput.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function ‘void pr_shell(FILE*, gmx::ArrayRef<const t_shell>)’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:126:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_shell>’ changed in GCC 7.1
126 | static void pr_shell(FILE* fplog, ArrayRef<const t_shell> shells)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function ‘real rms_force(const t_commrec*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const t_shell>, int, real*, real*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:778:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_shell>’ changed in GCC 7.1
778 | static real rms_force(const t_commrec* cr,
| ^~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_shell&}; _Tp = t_shell; _Alloc = std::allocator<t_shell>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_shell>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::make_local_shells(const t_commrec*, const t_mdatoms*, gmx_shellfc_t*)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_shell*, std::vector<t_shell> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationinputhandle.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function ‘gmx_shellfc_t* init_shell_flexcon(FILE*, const gmx_mtop_t*, int, int, bool, bool)’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:427:41: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_shell>’ changed in GCC 7.1
427 | pr_shell(fplog, shell);
| ~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:498:17: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_shell>’ changed in GCC 7.1
498 | pr_shell(debug, shell);
| ~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function ‘void init_adir(gmx_shellfc_t*, gmx::Constraints*, const t_inputrec*, const t_commrec*, int, int64_t, const t_mdatoms*, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, const real (*)[3], gmx::ArrayRef<const double>, real*)’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:828:13: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
828 | static void init_adir(gmx_shellfc_t* shfc,
| ^~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:890:18: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
890 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xCurrent,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
891 | shfc->adir_xnold.arrayRefWithPadding(), {}, box, lambda[efptBONDED],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
892 | &(dvdlambda[efptBONDED]), {}, computeVirial, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
893 | gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:894:18: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
894 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xCurrent,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
895 | shfc->adir_xnew.arrayRefWithPadding(), {}, box, lambda[efptBONDED],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
896 | &(dvdlambda[efptBONDED]), {}, computeVirial, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
897 | gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:910:18: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
910 | constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xOld, shfc->adir_xnew.arrayRefWithPadding(),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
911 | acc_dir, box, lambda[efptBONDED], &(dvdlambda[efptBONDED]), {}, computeVirial,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
912 | nullptr, gmx::ConstraintVariable::Deriv_FlexCon);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulatorbuilder.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function ‘void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx::ImdSession*, pull_t*, gmx_bool, int, const gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, const real (*)[3], gmx::ArrayRef<double>, history_t*, gmx::ForceBuffersView*, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, gmx_shellfc_t*, t_forcerec*, gmx::MdrunScheduleWorkload*, double, real*, gmx::VirtualSitesHandler*, const DDBalanceRegionHandler&)’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:915:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
915 | void relax_shell_flexcon(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1039:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1039 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, mdstep,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1040 | nrnb, wcycle, top, box, xPadded, hist, &forceViewInit, force_vir, md, enerd, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1041 | fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1042 | (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1055:32: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1055 | accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1047:18: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1047 | init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end, shfc->x_old.arrayRefWithPadding(),
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1048 | x, xPadded, force[Min], shfc->acc_dir, box, lambda, &dum);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1104:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1104 | vsite->construct(pos[Min], inputrec->delta_t, v, box);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1104:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1104:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1109:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1109 | init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1110 | shfc->x_old.arrayRefWithPadding(), x, posWithPadding[Min], force[Min],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1111 | shfc->acc_dir, box, lambda, &dum);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1126:17: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1126 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, 1, nrnb, wcycle,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1127 | top, box, posWithPadding[Try], hist, &forceViewTry, force_vir, md, enerd, lambda, fr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1128 | runScheduleWork, vsite, mu_tot, t, nullptr, shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1129:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
1129 | accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1138:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1138 | init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1139 | shfc->x_old.arrayRefWithPadding(), x, posWithPadding[Try], force[Try],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1140 | shfc->acc_dir, box, lambda, &dum);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp: In member function ‘void gmx::LegacySimulator::do_tpi()’:
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:605:26: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
605 | nbnxn_put_on_grid(fr->nbv.get(), box, 0, vzero, boxDiagonal, nullptr, { 0, a_tp0 }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
606 | fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:677:34: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
677 | nbnxn_put_on_grid(fr->nbv.get(), box, 1, x_init, x_init, nullptr, { a_tp0, a_tp1 },
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
678 | -1, fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:681:43: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
681 | fr->nbv->setAtomProperties(gmx::constArrayRefFromArray(mdatoms->typeA, mdatoms->nr),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
682 | gmx::constArrayRefFromArray(mdatoms->chargeA, mdatoms->nr),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
683 | fr->cginfo);
| ~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:681:43: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:738:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
738 | fr->nbv->convertCoordinates(AtomLocality::NonLocal, false, x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:738:40: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:756:21: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
756 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
757 | wcycle, &top, state_global->box, state_global->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
758 | &state_global->hist, &f.view(), force_vir, mdatoms, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
759 | state_global->lambda, fr, runScheduleWork, nullptr, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
760 | GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
761 | DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
In file included from /usr/include/c++/11/memory:76,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/11/bits/unique_ptr.h: In member function ‘int gmx::Mdrunner::mdrunner()’:
/usr/include/c++/11/bits/unique_ptr.h:962:30: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1245:51: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1245 | putUpdateGroupAtomsInSamePeriodicImage(*cr->dd, mtop, globalState->box, globalState->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1245:51: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1526:44: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
1526 | constructVirtualSitesGlobal(mtop, globalState->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function ‘void gmx::StatePropagatorDataGpu::copyCoordinatesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:129:6: note: parameter passing for argument of type ‘const gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
129 | void StatePropagatorDataGpu::copyCoordinatesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function ‘void gmx::StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:144:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
144 | void StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function ‘void gmx::StatePropagatorDataGpu::copyVelocitiesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:161:6: note: parameter passing for argument of type ‘const gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
161 | void StatePropagatorDataGpu::copyVelocitiesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function ‘void gmx::StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:177:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
177 | void StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function ‘void gmx::StatePropagatorDataGpu::copyForcesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:201:6: note: parameter passing for argument of type ‘const gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
201 | void StatePropagatorDataGpu::copyForcesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function ‘void gmx::StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)’:
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:226:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
226 | void StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintpotential.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp:38:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator<gmx::Site>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::Site>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In constructor ‘gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr<gmx::IRestraintPotential>, const std::vector<int>&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long int, std::allocator<long long int> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp: In static member function ‘static void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<double> >, int)’:
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:271:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
271 | void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
| ^~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx_file_position_t>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function ‘void writeXpmAxis(FILE*, const char*, gmx::ArrayRef<const double>)’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:830:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
830 | static void writeXpmAxis(FILE* out, const char* axis, ArrayRef<const real> label)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function ‘t_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:116:11: note: parameter passing for argument of type ‘gmx::ArrayRef<const t_mapping>’ changed in GCC 7.1
116 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:40:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_rgb>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_rgb>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘gmx::index search_col(t_psdata*, real, real, real)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:40:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::vector<t_matrix> read_xpm_matrix(const char*)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:46:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:46:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::internal::{anonymous}::computeMassesAndCharges(const gmx_mtop_t*, const gmx_ana_pos_t&, std::vector<double>*, std::vector<double>*)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:46:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:46:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::internal::SelectionData::initializeMassesAndCharges(const gmx_mtop_t*)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_simple.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
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CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o selection/CMakeFiles/scanner.dir/parser.cpp.o selection/CMakeFiles/scanner.dir/scanner.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.6.0.0 ../../lib/libgromacs_d.so.6 ../../lib/libgromacs_d.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target libgromacs
/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
Scanning dependencies of target gmx
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/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.6.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
Scanning dependencies of target nblib
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/usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/box.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/forcecalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/gmxcalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target gmx
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/gmxsetup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/integrator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/integrator.cpp
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp: In member function ‘void nblib::ForceCalculator::updatePairList(gmx::ArrayRef<const int>, gmx::ArrayRef<gmx::BasicVector<double> >, const nblib::Box&)’:
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:73:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
73 | void ForceCalculator::updatePairList(gmx::ArrayRef<const int> particleInfoAllVdW,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:77:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
77 | gmxForceCalculator_->setParticlesOnGrid(particleInfoAllVdW, coordinates, box);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:77:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp: In member function ‘void nblib::ForceCalculator::compute(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:63:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
63 | void ForceCalculator::compute(gmx::ArrayRef<const Vec3> coordinates, gmx::ArrayRef<Vec3> forces)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:63:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:70:33: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
70 | gmxForceCalculator_->compute(coordinates, forces);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:70:33: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/forcecalculator.cpp:70:33: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/interactions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/interactions.cpp
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp: In member function ‘void nblib::GmxForceCalculator::compute(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:70:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
70 | void GmxForceCalculator::compute(gmx::ArrayRef<const gmx::RVec> coordinateInput,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:70:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:74:29: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
74 | nbv_->convertCoordinates(gmx::AtomLocality::Local, false, coordinateInput);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:74:29: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp: In member function ‘void nblib::GmxForceCalculator::setParticlesOnGrid(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, const nblib::Box&)’:
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:82:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
82 | void GmxForceCalculator::setParticlesOnGrid(gmx::ArrayRef<const int> particleInfoAllVdw,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:82:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxcalculator.cpp:97:22: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
97 | nbnxn_put_on_grid(nbv_.get(), legacyBox, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
98 | { 0, int(coordinates.size()) }, particleDensity, particleInfoAllVdw,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
99 | coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/integrator.cpp: In member function ‘void nblib::LeapFrog::integrate(real, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, gmx::ArrayRef<const gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/api/nblib/integrator.cpp:63:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
63 | void LeapFrog::integrate(const real dt, gmx::ArrayRef<Vec3> x, gmx::ArrayRef<Vec3> v, gmx::ArrayRef<const Vec3> f)
| ^~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/integrator.cpp:63:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/integrator.cpp:63:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/molecules.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/particlesequencer.cpp
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp: In member function ‘void nblib::NbvSetupUtil::setAtomProperties(const std::vector<int>&, const std::vector<double>&)’:
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:172:49: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
172 | gmxForceCalculator_->nbv_->setAtomProperties(particleTypeIdOfAllParticles, charges, particleInfoAllVdw_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:172:49: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp: In member function ‘void nblib::NbvSetupUtil::setParticlesOnGrid(const std::vector<gmx::BasicVector<double> >&, const nblib::Box&)’:
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:298:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
298 | gmxForceCalculator_->setParticlesOnGrid(particleInfoAllVdw_, coordinates, box);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:298:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp: In member function ‘void nblib::NbvSetupUtil::setupNbnxmInstance(size_t, const nblib::NBKernelOptions&)’:
/<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:199:24: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
199 | nbnxn_atomdata_init(gmx::MDLogger(), atomData.get(), kernelSetup.kernelType, combinationRule,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | numParticleTypes, nonbondedParameters_, 1, numThreads);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/api/nblib/vector.h:47,
from /<<PKGBUILDDIR>>/api/nblib/gmxcalculator.h:52,
from /<<PKGBUILDDIR>>/api/nblib/gmxsetup.h:51,
from /<<PKGBUILDDIR>>/api/nblib/gmxsetup.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void nblib::NbvSetupUtil::setNonBondedParameters(const std::vector<nblib::ParticleType>&, const nblib::NonBondedInteractionMap&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/particletype.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/particletype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/simulationstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/topologyhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/topology.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/topology.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nblib::ParticleData}; _Tp = nblib::ParticleData; _Alloc = std::allocator<nblib::ParticleData>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::ParticleData>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In static member function ‘static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter> >(const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&)::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {0}]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::HarmonicAngleType&}; _Tp = nblib::HarmonicAngleType; _Alloc = std::allocator<nblib::HarmonicAngleType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ProperDihedral&}; _Tp = nblib::ProperDihedral; _Alloc = std::allocator<nblib::ProperDihedral>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> >::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::Default5Center&}; _Tp = nblib::Default5Center; _Alloc = std::allocator<nblib::Default5Center>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> >::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > >::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In static member function ‘static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter> >(const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&)::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {1}]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::CubicBondType&}; _Tp = nblib::CubicBondType; _Alloc = std::allocator<nblib::CubicBondType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In static member function ‘static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter> >(const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&)::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {2}]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::CubicBondType*, std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In static member function ‘static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter> >(const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&)::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {3}]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In static member function ‘static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter> >(const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&)::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, nblib::CubicBondType, nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >&}; unsigned int ...__indices = {4}]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ImproperDihedral&}; _Tp = nblib::ImproperDihedral; _Alloc = std::allocator<nblib::ImproperDihedral>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::RyckaertBellemanDihedral&}; _Tp = nblib::RyckaertBellemanDihedral; _Alloc = std::allocator<nblib::RyckaertBellemanDihedral>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> >::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void nblib::Molecule::addInteraction(const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const FiveCenterInteraction&)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::Default5Center*, std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In static member function ‘static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter> >(const std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&)::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>&}; unsigned int ...__indices = {0}]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::ProperDihedral*, std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In static member function ‘static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter> >(const std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&)::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>&}; unsigned int ...__indices = {1}]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::ImproperDihedral*, std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In static member function ‘static constexpr decltype(auto) std::__detail::__variant::__gen_vtable_impl<std::__detail::__variant::_Multi_array<_Result_type (*)(_Visitor, _Variants ...)>, std::integer_sequence<unsigned int, __indices ...> >::__visit_invoke(_Visitor&&, _Variants ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = nblib::Molecule::addInteractionImpl<std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ParticleNameParameter>, nblib::StrongType<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, nblib::ResidueNameParameter> >(const std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ParticleNameParameter>&, const nblib::StrongType<std::__cxx11::basic_string<char>, nblib::ResidueNameParameter>&)::<lambda(const auto:24&)>&; _Variants = {const std::variant<nblib::ProperDihedral, nblib::ImproperDihedral, nblib::RyckaertBellemanDihedral>&}; unsigned int ...__indices = {2}]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::RyckaertBellemanDihedral*, std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void nblib::Molecule::addInteraction(const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const nblib::ParticleIdentifier&, const ThreeCenterInteraction&)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::HarmonicAngleType*, std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/transformations.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/molecules.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘nblib::Molecule& nblib::Molecule::addParticle(const ParticleName&, const ResidueName&, const Charge&, const nblib::ParticleType&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::ParticleData*, std::vector<nblib::ParticleData> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp: In member function ‘void nblib::ListedForceCalculator::computeForcesAndEnergies(gmx::ArrayRef<const gmx::BasicVector<double> >, bool)’:
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:85:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
85 | void ListedForceCalculator::computeForcesAndEnergies(gmx::ArrayRef<const Vec3> x, bool usePbc)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp: In member function ‘void nblib::ListedForceCalculator::compute(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, bool)’:
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:137:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
137 | void ListedForceCalculator::compute(gmx::ArrayRef<const Vec3> coordinates, gmx::ArrayRef<Vec3> forces, bool usePbc)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:137:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:151:29: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
151 | computeForcesAndEnergies(coordinates, usePbc);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp: In member function ‘void nblib::ListedForceCalculator::compute(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, nblib::ListedForceCalculator::EnergyType&, bool)’:
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:159:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
159 | void ListedForceCalculator::compute(gmx::ArrayRef<const Vec3> coordinates,
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:159:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:164:12: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
164 | compute(coordinates, forces, usePbc);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:164:12: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/calculator.cpp:164:12: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/g++-11 -DGMX_DOUBLE=1 -Dnblib_EXPORTS -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/setup.cpp
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>(const std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>(const std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>(const std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/util/setup.cpp: In function ‘bool nblib::isRealValued(gmx::ArrayRef<const gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/api/nblib/util/setup.cpp:124:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
124 | bool isRealValued(gmx::ArrayRef<const Vec3> values)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/util/setup.cpp: In function ‘void nblib::zeroCartesianArray(gmx::ArrayRef<gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/api/nblib/util/setup.cpp:139:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
139 | void zeroCartesianArray(gmx::ArrayRef<Vec3> cartesianArray)
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘_ForwardIterator std::__upper_bound(_ForwardIterator, _ForwardIterator, const _Tp&, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Tp = std::tuple<nblib::ProperDihedral, unsigned int>; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>(const std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:2028:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
2028 | __upper_bound(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:2028:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>(const std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>(const std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::ProperDihedral, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>(const std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>(const std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>(const std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>(const std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::Default5Center>(const std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>(const std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>(const std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>(const std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::Default5Center>(const std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >’ changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::CubicBondType, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>(const std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::HarmonicAngleType, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>(const std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::ImproperDihedral, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>(const std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::Default5Center, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::Default5Center>(const std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ParticleType&}; _Tp = nblib::ParticleType; _Alloc = std::allocator<nblib::ParticleType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::ParticleType>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::CubicBondType&}; _Tp = nblib::CubicBondType; _Alloc = std::allocator<nblib::CubicBondType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::CubicBondType]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::CubicBondType*, std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::HarmonicAngleType&}; _Tp = nblib::HarmonicAngleType; _Alloc = std::allocator<nblib::HarmonicAngleType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::HarmonicAngleType]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::HarmonicAngleType*, std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ProperDihedral&}; _Tp = nblib::ProperDihedral; _Alloc = std::allocator<nblib::ProperDihedral>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::ProperDihedral]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::ProperDihedral*, std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ImproperDihedral&}; _Tp = nblib::ImproperDihedral; _Alloc = std::allocator<nblib::ImproperDihedral>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::ImproperDihedral]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::ImproperDihedral*, std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::RyckaertBellemanDihedral&}; _Tp = nblib::RyckaertBellemanDihedral; _Alloc = std::allocator<nblib::RyckaertBellemanDihedral>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::RyckaertBellemanDihedral]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::RyckaertBellemanDihedral*, std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::Default5Center&}; _Tp = nblib::Default5Center; _Alloc = std::allocator<nblib::Default5Center>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::Default5Center]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::Default5Center*, std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1642 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>(const std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>(const std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>(const std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>(const std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>(const std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>]’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>]’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::G96BondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::CubicBondType>(const std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::CubicBondType]’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::CubicBondType, unsigned int>*, std::vector<std::tuple<nblib::CubicBondType, unsigned int>, std::allocator<std::tuple<nblib::CubicBondType, unsigned int> > > >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::CubicBondType*, std::vector<nblib::CubicBondType, std::allocator<nblib::CubicBondType> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>]’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::FENEBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>]’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HalfAttractiveQuarticBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::HarmonicAngleType>(const std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::HarmonicAngleType]’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::HarmonicAngleType, unsigned int>*, std::vector<std::tuple<nblib::HarmonicAngleType, unsigned int>, std::allocator<std::tuple<nblib::HarmonicAngleType, unsigned int> > > >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::HarmonicAngleType*, std::vector<nblib::HarmonicAngleType, std::allocator<nblib::HarmonicAngleType> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ProperDihedral>(const std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::ProperDihedral]’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:2144:37: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
2144 | = std::__upper_bound(++__middle, __first, __val, __comp_val_it);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::ProperDihedral*, std::vector<nblib::ProperDihedral, std::allocator<nblib::ProperDihedral> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_algo.h:2108:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ProperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ProperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ProperDihedral, unsigned int> > > >’ changed in GCC 7.1
2108 | return std::__upper_bound(__first, __last, __val,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2109 | __gnu_cxx::__ops::__val_comp_iter(__comp));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::ImproperDihedral>(const std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::ImproperDihedral]’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::ImproperDihedral, unsigned int>*, std::vector<std::tuple<nblib::ImproperDihedral, unsigned int>, std::allocator<std::tuple<nblib::ImproperDihedral, unsigned int> > > >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::ImproperDihedral*, std::vector<nblib::ImproperDihedral, std::allocator<nblib::ImproperDihedral> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::RyckaertBellemanDihedral>(const std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::RyckaertBellemanDihedral]’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>*, std::vector<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int>, std::allocator<std::tuple<nblib::RyckaertBellemanDihedral, unsigned int> > > >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::RyckaertBellemanDihedral*, std::vector<nblib::RyckaertBellemanDihedral, std::allocator<nblib::RyckaertBellemanDihedral> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::Default5Center>(const std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::Default5Center]’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::Default5Center, unsigned int>*, std::vector<std::tuple<nblib::Default5Center, unsigned int>, std::allocator<std::tuple<nblib::Default5Center, unsigned int> > > >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/api/nblib/topology.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::Default5Center*, std::vector<nblib::Default5Center, std::allocator<nblib::Default5Center> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘nblib::Topology nblib::TopologyBuilder::buildTopology()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::ParticleType*, std::vector<nblib::ParticleType> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1
/usr/bin/g++-11 -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib.so.0 -o ../../lib/libnblib.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/forcecalculator.cpp.o CMakeFiles/nblib.dir/gmxcalculator.cpp.o CMakeFiles/nblib.dir/gmxsetup.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o ../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib.so.0.1.0 ../../lib/libnblib.so.0 ../../lib/libnblib.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target nblib
/usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake --color=
Scanning dependencies of target argon-forces-integration
Scanning dependencies of target methane-water-integration
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples && /usr/bin/g++-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples && /usr/bin/g++-11 -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/stl_vector.h:625:7: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/stl_vector.h:625:7: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp: In function ‘int main()’:
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:89:5: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
89 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:96:5: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
96 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:103:5: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
103 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:120:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
120 | forceCalculator.compute(simState.coordinates(), userForces);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:120:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:120:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:129:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
129 | integrator.integrate(1.0, simState.coordinates(), simState.velocities(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:129:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:129:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/argon-forces-integration.cpp:129:25: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp: In function ‘int main()’:
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:157:5: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
157 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:172:5: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
172 | };
| ^
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:201:32: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
201 | forceCalculator.compute(simulationState.coordinates(), simulationState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:201:32: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:201:32: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:203:38: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
203 | listedForceCalculator.compute(simulationState.coordinates(), simulationState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:203:38: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:203:38: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:206:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
206 | integrator.integrate(1.0, simulationState.coordinates(), simulationState.velocities(),
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
207 | simulationState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:206:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:206:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/samples/methane-water-integration.cpp:206:29: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -o ../../../bin/argon-forces-integration ../../../lib/libnblib.so.0.1.0 -Wl,-rpath-link,/<<PKGBUILDDIR>>/build/basic-dp/lib
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/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -o ../../../bin/methane-water-integration ../../../lib/libnblib.so.0.1.0 -Wl,-rpath-link,/<<PKGBUILDDIR>>/build/basic-dp/lib
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
[ 4%] Built target thread_mpi
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[ 65%] Built target nblib
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[ 66%] Built target argon-forces-integration
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++17 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/g++-11 -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi_printer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata_xml.cpp
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cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/testsystems.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
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/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.6.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulatorcomparison.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.6.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 69%] Built target testutils-test
/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp: In member function ‘virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:234:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
234 | bias.calcForceAndUpdateBias(coordValue, {}, {}, &potential, &potentialJump, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
235 | nullptr, step, step, seed_, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:234:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:234:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp: In member function ‘virtual void gmx::test::BiasTest_DetectsCovering_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:319:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
319 | bias.calcForceAndUpdateBias(coordValue, {}, {}, &potential, &potentialJump, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
320 | nullptr, step, step, params.awhParams.seed, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:319:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:319:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target mdrun_test_infrastructure
/usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target density_fitting_applied_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/dimparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:61,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasgrid.cpp:37:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::test::biasGridTest_neighborhood_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasstate.cpp:37:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In constructor ‘gmx::test::BiasStateTest::BiasStateTest()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energydrifttracker.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp
/usr/include/c++/11/bits/vector.tcc: In constructor ‘gmx::test::BiasFepLambdaStateTest::BiasFepLambdaStateTest()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp: In member function ‘virtual void gmx::test::BiasFepLambdaStateTest_ForcesBiasPmf_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:227:76: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
227 | gmx::ArrayRef<const double> biasForce = bias.calcForceAndUpdateBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^
228 | coordValue, neighborLambdaEnergies, neighborLambdaDhdl, &potential, &potentialJump,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | nullptr, nullptr, step * mdTimeStep, step, seed_, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:227:76: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:227:76: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::test::BiasFepLambdaStateTest_DetectsCovering_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:307:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
307 | bias.calcForceAndUpdateBias(coordValue, neighborLambdaEnergies, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
308 | &potential, &potentialJump, nullptr, nullptr, step, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
309 | params.awhParams.seed, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:307:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:307:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasgrid.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.6.0.0 ../../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.6.0.0 ../../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target density_fitting_applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/freeenergyparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target listed_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_grp_tcstat>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In constructor ‘gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:49:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::test::{anonymous}::iListInput; _Alloc = std::allocator<gmx::test::{anonymous}::iListInput>]’:
/usr/include/c++/11/bits/stl_vector.h:625:7: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:63,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:56:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<typename testing::internal::IteratorTraits<Iterator>::value_type> testing::ValuesIn(ForwardIterator, ForwardIterator) [with ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >]’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:304:1: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
304 | ValuesIn(ForwardIterator begin, ForwardIterator end) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:304:1: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_AngleListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_DihedralListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_PolarizeListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_RestraintsListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_AngleZeroListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_BondListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<float>, gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_BondZeroLengthListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’:
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:646:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
646 | std::vector<iListInput> c_InputBonds = {
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:661:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
661 | std::vector<iListInput> c_InputAngles = {
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:685:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
685 | std::vector<iListInput> c_InputDihs = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:695:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
695 | std::vector<iListInput> c_InputPols = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:705:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
705 | std::vector<iListInput> c_InputRestraints = {
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:715:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
715 | std::vector<iListInput> c_InputBondsZeroLength = {
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:720:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
720 | std::vector<iListInput> c_InputAnglesZeroAngle = {
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test-shared
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/listed_forces-test.dir/bonded.cpp.o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target listed_forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target onlinehelp-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
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Scanning dependencies of target domdec-mpi-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/haloexchange_mpi.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/listoflists.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target domdec-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target domdec-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mdmodulenotification-impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp
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/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target mdlib-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
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make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target fft-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_availability.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/range.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/range.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_stream_manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/device_management.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/template_mp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/cpuinfo.cpp.o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/hardware-test.dir/device_management.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
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Scanning dependencies of target math-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 74%] Built target ewald-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests/checkpointdata.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
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/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target onlinehelp-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests/forcebuffers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target mdspan-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target mdtypes-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pbcutil-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/optimization.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/optimization.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/com.cpp.o CMakeFiles/pbcutil-test.dir/mshift.cpp.o CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target pbcutil-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/bits/random.h:34,
from /usr/include/c++/11/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]’:
/usr/include/c++/11/bits/stl_vector.h:625:7: note: parameter passing for argument of type ‘std::initializer_list<long long unsigned int>’ changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/bits/random.h:34,
from /usr/include/c++/11/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ThreeFry2x64Test_InternalCounterSequence_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ThreeFry2x64Test_Fast_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ThreeFry2x64Test_Default_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ThreeFry2x64Test_Using40Rounds_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’:
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type ‘std::initializer_list<long long unsigned int>’ changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type ‘std::initializer_list<long long unsigned int>’ changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type ‘std::initializer_list<long long unsigned int>’ changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target options-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = const double]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘std::enable_if_t<is_same_v<typename std::remove_const<_Tp>::type, typename std::remove_const<U>::type>, void> gmx::test::compareViewsIgnoreConst(gmx::ArrayRef<T>, gmx::ArrayRef<U>) [with T = double; U = const double]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
100 | compareViewsIgnoreConst(ArrayRef<T> input, ArrayRef<U> output)
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
111 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘std::enable_if_t<is_same_v<typename std::remove_const<_Tp>::type, typename std::remove_const<U>::type>, void> gmx::test::compareViewsIgnoreConst(gmx::ArrayRef<T>, gmx::ArrayRef<U>) [with T = gmx::BasicVector<double>; U = const gmx::BasicVector<double>]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
100 | compareViewsIgnoreConst(ArrayRef<T> input, ArrayRef<U> output)
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = const gmx::BasicVector<double>]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function ‘void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]’:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function ‘void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]’:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target random-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function ‘void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]’:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function ‘void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]’:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
Scanning dependencies of target topology-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/neldermead.cpp.o CMakeFiles/math-test.dir/optimization.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/topology-test.dir/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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[ 82%] Built target pull-test
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/mp11.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/mp11.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 82%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/idef.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 83%] Built target topology-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx3-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx2-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target gmxana-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx1-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target pdb2gmx3-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target pdb2gmx2-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target pdb2gmx1-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 87%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 87%] Built target analysisdata-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target gmxpreprocess-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/helpwriting.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target energyanalysis-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/checkpoint.cpp
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/helpwriting.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-modules-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target coordinateio-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-test
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
[ 90%] Built target mdrun-modules-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-pme-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In static member function ‘static void gmx::test::XvgioTest::compareValues(gmx::basic_mdspan<const double, gmx::extents<-1, -1> >, gmx::basic_mdspan<const double, gmx::extents<-1, -1> >)’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:75:17: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
75 | static void compareValues(basic_mdspan<const double, dynamicExtents2D> ref,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:75:17: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function ‘virtual void gmx::test::XvgioTest_readXvgIgnoreCommentLineWorks_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:150:18: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
150 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:150:18: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function ‘virtual void gmx::test::XvgioTest_readXvgRealWorks_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:132:18: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
132 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:132:18: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function ‘virtual void gmx::test::XvgioTest_readXvgIntWorks_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:113:18: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
113 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:113:18: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pme-test.dir/link.txt --verbose=1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/checkpoint.cpp.o CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/xvgio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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[ 90%] Built target mdrun-pme-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
[ 91%] Built target fileio-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-io-test
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/ewaldsurfaceterm.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multiple_time_stepping.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-simulator-comparison-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target mdrun-mpi-coordination-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-tpi-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-pme-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target mdrun-tpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target mdrun-mpi-pme-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunfep-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/freeenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target mdrun-output-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake --color=
Scanning dependencies of target nblib-setup-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/box.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target mdrun-non-integrator-test
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target nblib-integrator-test
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cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/particletype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunfep-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrunfep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake --color=
Scanning dependencies of target nblib-integration-test
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cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/pbcholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/nbnxnsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/molecules.cpp
/usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target nblib-listed-forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/bondtypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target nblib-integrator-test
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/simstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/helpers.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/kernels.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target nblib-integration-test
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/util/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake --color=
Scanning dependencies of target nblib-util-test
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cd /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/tests/setup.cpp
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/tests/traits.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-util-test.dir/setup.cpp.o CMakeFiles/nblib-util-test.dir/traits.cpp.o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target nblib-util-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/conversions.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-setup-test.dir/box.cpp.o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o CMakeFiles/nblib-setup-test.dir/topology.cpp.o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/transformations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target mdrunutility-test
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target trajectoryanalysis-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target nblib-listed-forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
/usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/api/nblib /<<PKGBUILDDIR>>/build/basic/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake --color=
Scanning dependencies of target nblib-tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'.
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[ 97%] Built target nblib-tests
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
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make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target commandline-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
(cd build/basic; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: NbLibListedForcesTests
1: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibListedForcesTests.xml"
1: Test timeout computed to be: 600
1: [==========] Running 23 tests from 9 test cases.
1: [----------] Global test environment set-up.
1: [----------] 5 tests from NBlibTest
1: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks
1: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms)
1: [ RUN ] NBlibTest.BondTypesLessThanWorks
1: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms)
1: [ RUN ] NBlibTest.CanSplitListedWork
1: [ OK ] NBlibTest.CanSplitListedWork (0 ms)
1: [ RUN ] NBlibTest.ListedForceBuffer
1: [ OK ] NBlibTest.ListedForceBuffer (0 ms)
1: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct
1: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms)
1: [----------] 5 tests from NBlibTest (0 ms total)
1:
1: [----------] 1 test from Kernels
1: [ RUN ] Kernels.HarmonicScalarKernelCanCompute
1: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms)
1: [----------] 1 test from Kernels (0 ms total)
1:
1: [----------] 5 tests from ListedExampleData
1: [ RUN ] ListedExampleData.ComputeHarmonicBondForces
1: [ OK ] ListedExampleData.ComputeHarmonicBondForces (1 ms)
1: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies
1: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (1 ms)
1: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces
1: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms)
1: [ RUN ] ListedExampleData.CanReduceForces
1: [ OK ] ListedExampleData.CanReduceForces (0 ms)
1: [ RUN ] ListedExampleData.CanReduceEnergies
1: [ OK ] ListedExampleData.CanReduceEnergies (0 ms)
1: [----------] 5 tests from ListedExampleData (2 ms total)
1:
1: [----------] 1 test from LinearChainDataFixture
1: [ RUN ] LinearChainDataFixture.Multithreading
1: [ OK ] LinearChainDataFixture.Multithreading (7 ms)
1: [----------] 1 test from LinearChainDataFixture (7 ms total)
1:
1: [----------] 1 test from ListedShims
1: [ RUN ] ListedShims.ParameterConversion
1: [ OK ] ListedShims.ParameterConversion (0 ms)
1: [----------] 1 test from ListedShims (0 ms total)
1:
1: [----------] 1 test from ListedTransformations
1: [ RUN ] ListedTransformations.SortInteractionIndices
1: [ OK ] ListedTransformations.SortInteractionIndices (0 ms)
1: [----------] 1 test from ListedTransformations (0 ms total)
1:
1: [----------] 3 tests from FourCenter/ProperDihedralTest
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/0
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/0 (0 ms)
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/1
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/1 (1 ms)
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/2
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/2 (0 ms)
1: [----------] 3 tests from FourCenter/ProperDihedralTest (1 ms total)
1:
1: [----------] 3 tests from TwoCenter/HarmonicBondTest
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/0
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/0 (0 ms)
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/1
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/1 (1 ms)
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/2
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/2 (0 ms)
1: [----------] 3 tests from TwoCenter/HarmonicBondTest (1 ms total)
1:
1: [----------] 3 tests from ThreeCenter/HarmonicAngleTest
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/0
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/0 (0 ms)
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/1
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/1 (1 ms)
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/2
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/2 (0 ms)
1: [----------] 3 tests from ThreeCenter/HarmonicAngleTest (1 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 23 tests from 9 test cases ran. (12 ms total)
1: [ PASSED ] 23 tests.
1/65 Test #1: NbLibListedForcesTests ................ Passed 1.84 sec
test 2
Start 2: NbLibSamplesTestArgon
2: Test command: /<<PKGBUILDDIR>>/build/basic/bin/argon-forces-integration
2: Test timeout computed to be: 1500
2: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000
2: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191
2: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000
2: final position of particle 0: x 0.789162 y 1.271508 z 0.819867
2/65 Test #2: NbLibSamplesTestArgon ................. Passed 0.06 sec
test 3
Start 3: NbLibSamplesTestMethaneWater
3: Test command: /<<PKGBUILDDIR>>/build/basic/bin/methane-water-integration
3: Test timeout computed to be: 1500
3: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000
3: final position of particle 9: x 0.132611 y 4.369854 z 5.148869
3/65 Test #3: NbLibSamplesTestMethaneWater .......... Passed 0.05 sec
test 4
Start 4: NbLibUtilTests
4: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-util-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibUtilTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 16 tests from 2 test cases.
4: [----------] Global test environment set-up.
4: [----------] 6 tests from NBlibTest
4: [ RUN ] NBlibTest.isRealValued
4: [ OK ] NBlibTest.isRealValued (0 ms)
4: [ RUN ] NBlibTest.checkNumericValuesHasNan
4: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms)
4: [ RUN ] NBlibTest.checkNumericValuesHasInf
4: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms)
4: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (1 ms)
4: [ RUN ] NBlibTest.generateVelocitySize
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.generateVelocitySize (0 ms)
4: [ RUN ] NBlibTest.generateVelocityCheckNumbers
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms)
4: [----------] 6 tests from NBlibTest (1 ms total)
4:
4: [----------] 10 tests from NblibTraitsUtils
4: [ RUN ] NblibTraitsUtils.FuseTwo
4: [ OK ] NblibTraitsUtils.FuseTwo (0 ms)
4: [ RUN ] NblibTraitsUtils.Fuse
4: [ OK ] NblibTraitsUtils.Fuse (0 ms)
4: [ RUN ] NblibTraitsUtils.Repeat
4: [ OK ] NblibTraitsUtils.Repeat (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTuple1
4: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTuple2
4: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeList1
4: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeList2
4: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms)
4: [ RUN ] NblibTraitsUtils.Contains
4: [ OK ] NblibTraitsUtils.Contains (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated
4: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated
4: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms)
4: [----------] 10 tests from NblibTraitsUtils (1 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 16 tests from 2 test cases ran. (2 ms total)
4: [ PASSED ] 16 tests.
4/65 Test #4: NbLibUtilTests ........................ Passed 0.05 sec
test 5
Start 5: NbLibSetupTests
5: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-setup-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibSetupTests.xml"
5: Test timeout computed to be: 600
5: [==========] Running 39 tests from 1 test case.
5: [----------] Global test environment set-up.
5: [----------] 39 tests from NBlibTest
5: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN
5: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms)
5: [ RUN ] NBlibTest.CubicBoxCannotHaveInf
5: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms)
5: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN
5: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms)
5: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf
5: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms)
5: [ RUN ] NBlibTest.CubicBoxWorks
5: [ OK ] NBlibTest.CubicBoxWorks (0 ms)
5: [ RUN ] NBlibTest.NonBondedForceParamsCorrect
5: [ OK ] NBlibTest.NonBondedForceParamsCorrect (1 ms)
5: [ RUN ] NBlibTest.CanMergeInteractions
5: [ OK ] NBlibTest.CanMergeInteractions (0 ms)
5: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed
5: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms)
5: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed
5: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms)
5: [ RUN ] NBlibTest.PbcHolderWorks
5: [ OK ] NBlibTest.PbcHolderWorks (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms)
5: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule
5: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms)
5: [ RUN ] NBlibTest.CanConstructExclusionListFromNames
5: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms)
5: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed
5: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (1 ms)
5: [ RUN ] NBlibTest.AtWorks
5: [ OK ] NBlibTest.AtWorks (0 ms)
5: [ RUN ] NBlibTest.AtThrows
5: [ OK ] NBlibTest.AtThrows (0 ms)
5: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass
5: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms)
5: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass
5: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms)
5: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName
5: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms)
5: [ RUN ] NBlibTest.CanAddInteractions
5: [ OK ] NBlibTest.CanAddInteractions (0 ms)
5: [ RUN ] NBlibTest.TopologyHasNumParticles
5: [ OK ] NBlibTest.TopologyHasNumParticles (1 ms)
5: [ RUN ] NBlibTest.TopologyHasCharges
5: [ OK ] NBlibTest.TopologyHasCharges (0 ms)
5: [ RUN ] NBlibTest.TopologyHasMasses
5: [ OK ] NBlibTest.TopologyHasMasses (0 ms)
5: [ RUN ] NBlibTest.TopologyHasParticleTypes
5: [ OK ] NBlibTest.TopologyHasParticleTypes (1 ms)
5: [ RUN ] NBlibTest.TopologyHasParticleTypeIds
5: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms)
5: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType
5: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms)
5: [ RUN ] NBlibTest.TopologyHasExclusions
5: [ OK ] NBlibTest.TopologyHasExclusions (0 ms)
5: [ RUN ] NBlibTest.TopologyHasSequencing
5: [ OK ] NBlibTest.TopologyHasSequencing (1 ms)
5: [ RUN ] NBlibTest.TopologyCanAggregateBonds
5: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms)
5: [ RUN ] NBlibTest.TopologyCanSequencePairIDs
5: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms)
5: [ RUN ] NBlibTest.TopologySequenceIdThrows
5: No particle O-Atom in residue SOL in molecule SOL found
5: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms)
5: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds
5: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms)
5: [ RUN ] NBlibTest.TopologyListedInteractions
5: [ OK ] NBlibTest.TopologyListedInteractions (1 ms)
5: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes
5: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (1 ms)
5: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows
5: No particle Iron in residue SOL in molecule SOL found
5: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms)
5: [ RUN ] NBlibTest.toGmxExclusionBlockWorks
5: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms)
5: [----------] 39 tests from NBlibTest (7 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 39 tests from 1 test case ran. (7 ms total)
5: [ PASSED ] 39 tests.
5/65 Test #5: NbLibSetupTests ....................... Passed 0.05 sec
test 6
Start 6: NbLibIntegrationTests
6: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-integration-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibIntegrationTests.xml"
6: Test timeout computed to be: 600
6: [==========] Running 19 tests from 1 test case.
6: [----------] Global test environment set-up.
6: [----------] 19 tests from NBlibTest
6: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute
6: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (2 ms)
6: [ RUN ] NBlibTest.CanSetupStepWorkload
6: [ OK ] NBlibTest.CanSetupStepWorkload (0 ms)
6: [ RUN ] NBlibTest.GmxForceCalculatorCanSetupInteractionConst
6: [ OK ] NBlibTest.GmxForceCalculatorCanSetupInteractionConst (1 ms)
6: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect
6: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (1 ms)
6: [ RUN ] NBlibTest.ExpectedNumberOfForces
6: [ OK ] NBlibTest.ExpectedNumberOfForces (1 ms)
6: [ RUN ] NBlibTest.CanIntegrateSystem
6: [ OK ] NBlibTest.CanIntegrateSystem (1 ms)
6: [ RUN ] NBlibTest.UpdateChangesForces
6: [ OK ] NBlibTest.UpdateChangesForces (2 ms)
6: [ RUN ] NBlibTest.ArgonForcesAreCorrect
6: [ OK ] NBlibTest.ArgonForcesAreCorrect (1 ms)
6: [ RUN ] NBlibTest.CanConstructNbvSetupUtil
6: [ OK ] NBlibTest.CanConstructNbvSetupUtil (0 ms)
6: [ RUN ] NBlibTest.CanConstructSimulationState
6: [ OK ] NBlibTest.CanConstructSimulationState (0 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN
6: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (1 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF
6: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN
6: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF
6: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms)
6: [ RUN ] NBlibTest.SimulationStateCanMove
6: [ OK ] NBlibTest.SimulationStateCanMove (1 ms)
6: [ RUN ] NBlibTest.SimulationStateCanAssign
6: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasBox
6: [ OK ] NBlibTest.SimulationStateHasBox (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates
6: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities
6: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms)
6: [----------] 19 tests from NBlibTest (11 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 19 tests from 1 test case ran. (12 ms total)
6: [ PASSED ] 19 tests.
6/65 Test #6: NbLibIntegrationTests ................. Passed 0.04 sec
test 7
Start 7: NbLibIntegratorTests
7: Test command: /<<PKGBUILDDIR>>/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/NbLibIntegratorTests.xml"
7: Test timeout computed to be: 600
7: [==========] Running 1 test from 1 test case.
7: [----------] Global test environment set-up.
7: [----------] 1 test from NBlibTest
7: [ RUN ] NBlibTest.IntegratorWorks
7: [ OK ] NBlibTest.IntegratorWorks (1 ms)
7: [----------] 1 test from NBlibTest (1 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 1 test from 1 test case ran. (1 ms total)
7: [ PASSED ] 1 test.
7/65 Test #7: NbLibIntegratorTests .................. Passed 0.03 sec
test 8
Start 8: TestUtilsUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 59 tests from 5 test cases.
8: [----------] Global test environment set-up.
8: [----------] 10 tests from InteractiveTestHelperTest
8: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
8: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
8: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
8: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
8: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms)
8: [----------] 10 tests from InteractiveTestHelperTest (9 ms total)
8:
8: [----------] 34 tests from ReferenceDataTest
8: [ RUN ] ReferenceDataTest.HandlesSimpleData
8: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
8: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
8: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesStringBlockData
8: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesVectorData
8: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceData
8: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
8: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesIncorrectData
8: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
8: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMissingData
8: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedData
8: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
8: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
8: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnys
8: [ OK ] ReferenceDataTest.HandlesAnys (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
8: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
8: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
8: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
8: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
8: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
8: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
8: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
8: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
8: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
8: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
8: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
8: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
8: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
8: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesReadingValues
8: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
8: [----------] 34 tests from ReferenceDataTest (21 ms total)
8:
8: [----------] 7 tests from FloatingPointDifferenceTest
8: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
8: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
8: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
8: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
8: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
8: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
8: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
8: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
8: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
8:
8: [----------] 4 tests from FloatingPointToleranceTest
8: [ RUN ] FloatingPointToleranceTest.UlpTolerance
8: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
8: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
8: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
8: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
8: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
8: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
8: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
8: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
8:
8: [----------] 4 tests from XvgTests
8: [ RUN ] XvgTests.CreateFile
8: [ OK ] XvgTests.CreateFile (1 ms)
8: [ RUN ] XvgTests.CheckMissing
8: [ OK ] XvgTests.CheckMissing (1 ms)
8: [ RUN ] XvgTests.CheckExtra
8: [ OK ] XvgTests.CheckExtra (1 ms)
8: [ RUN ] XvgTests.ReadIncorrect
8: [ OK ] XvgTests.ReadIncorrect (2 ms)
8: [----------] 4 tests from XvgTests (5 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 59 tests from 5 test cases ran. (35 ms total)
8: [ PASSED ] 59 tests.
8/65 Test #8: TestUtilsUnitTests .................... Passed 0.07 sec
test 9
Start 9: TestUtilsMpiUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 1 test from 1 test case.
9: [----------] Global test environment set-up.
9: [----------] 1 test from MpiSelfTest
9: [ RUN ] MpiSelfTest.Runs
9: [ OK ] MpiSelfTest.Runs (1 ms)
9: [----------] 1 test from MpiSelfTest (1 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 1 test from 1 test case ran. (2 ms total)
9: [ PASSED ] 1 test.
9/65 Test #9: TestUtilsMpiUnitTests ................. Passed 0.03 sec
test 10
Start 10: UtilityUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 373 tests from 61 test cases.
10: [----------] Global test environment set-up.
10: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.Move
10: [ OK ] AllocatorTest/0.Move (0 ms)
10: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/0 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<float, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.Move
10: [ OK ] AllocatorTest/1.Move (0 ms)
10: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/1 (0 ms total)
10:
10: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.Move
10: [ OK ] AllocatorTest/2.Move (0 ms)
10: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/2 (0 ms total)
10:
10: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.Move
10: [ OK ] AllocatorTest/3.Move (0 ms)
10: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/3 (0 ms total)
10:
10: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/4.Move
10: [ OK ] AllocatorTest/4.Move (0 ms)
10: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/4 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/5.Move
10: [ OK ] AllocatorTest/5.Move (0 ms)
10: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/5 (1 ms total)
10:
10: [----------] 1 test from AllocatorUntypedTest
10: [ RUN ] AllocatorUntypedTest.Comparison
10: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
10: [----------] 1 test from AllocatorUntypedTest (0 ms total)
10:
10: [----------] 1 test from EmptyArrayRefTest
10: [ RUN ] EmptyArrayRefTest.IsEmpty
10: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
10: [----------] 1 test from EmptyArrayRefTest (0 ms total)
10:
10: [----------] 1 test from EmptyConstArrayRefTest
10: [ RUN ] EmptyConstArrayRefTest.IsEmpty
10: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
10: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
10: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/0 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
10: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/1 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
10: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/2 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
10: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/3 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
10: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/4 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
10: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/5 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
10: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/6 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
10: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/7 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
10: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
10: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/9 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
10: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
10: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/11 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
10: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/12 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
10: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (1 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/13 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
10: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
10: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/15 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
10: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/16 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
10: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/17 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
10: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/18 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
10: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/19 (0 ms total)
10:
10: [----------] 2 tests from CStringUtilityTest
10: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
10: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
10: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
10: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
10: [----------] 2 tests from CStringUtilityTest (0 ms total)
10:
10: [----------] 2 tests from DefaultInitializationAllocator
10: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
10: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
10: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
10: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
10: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
10:
10: [----------] 4 tests from EnumerationHelpersTest
10: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
10: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
10: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
10: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
10: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
10: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
10: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
10: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
10: [----------] 4 tests from EnumerationHelpersTest (0 ms total)
10:
10: [----------] 9 tests from FixedCapacityVectorTest
10: [ RUN ] FixedCapacityVectorTest.IsEmpty
10: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
10: [ RUN ] FixedCapacityVectorTest.PushWorks
10: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.PopWorks
10: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ClearWorks
10: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
10: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.AtThrows
10: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms)
10: [ RUN ] FixedCapacityVectorTest.IteratorWorks
10: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
10: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
10: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
10: [----------] 9 tests from FixedCapacityVectorTest (1 ms total)
10:
10: [----------] 5 tests from InMemorySerializerTest
10: [ RUN ] InMemorySerializerTest.Roundtrip
10: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
10: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
10: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
10: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
10: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.SizeIsCorrect
10: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
10: [----------] 5 tests from InMemorySerializerTest (0 ms total)
10:
10: [----------] 4 tests from KeyValueTreeSerializerTest
10: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
10: [ OK ] KeyValueTreeSerializerTest.EmptyTree (20 ms)
10: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
10: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms)
10: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
10: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms)
10: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
10: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms)
10: [----------] 4 tests from KeyValueTreeSerializerTest (21 ms total)
10:
10: [----------] 6 tests from TreeValueTransformTest
10: [ RUN ] TreeValueTransformTest.SimpleTransforms
10: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms)
10: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
10: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (1 ms)
10: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
10: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms)
10: [ RUN ] TreeValueTransformTest.ObjectFromString
10: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms)
10: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
10: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (1 ms)
10: [ RUN ] TreeValueTransformTest.ScopedTransformRules
10: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms)
10: [----------] 6 tests from TreeValueTransformTest (2 ms total)
10:
10: [----------] 1 test from TreeValueTransformErrorTest
10: [ RUN ] TreeValueTransformErrorTest.ConversionError
10: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms)
10: [----------] 1 test from TreeValueTransformErrorTest (0 ms total)
10:
10: [----------] 9 tests from ListOfLists
10: [ RUN ] ListOfLists.EmptyListOfListsWorks
10: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms)
10: [ RUN ] ListOfLists.AppendWorks
10: [ OK ] ListOfLists.AppendWorks (1 ms)
10: [ RUN ] ListOfLists.EmptyListWorks
10: [ OK ] ListOfLists.EmptyListWorks (0 ms)
10: [ RUN ] ListOfLists.AppendAccessWorks
10: [ OK ] ListOfLists.AppendAccessWorks (0 ms)
10: [ RUN ] ListOfLists.ClearWorks
10: [ OK ] ListOfLists.ClearWorks (0 ms)
10: [ RUN ] ListOfLists.OutOfRangeAccessThrows
10: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms)
10: [ RUN ] ListOfLists.FrontAndBackWork
10: [ OK ] ListOfLists.FrontAndBackWork (0 ms)
10: [ RUN ] ListOfLists.ExtractsAndRestores
10: [ OK ] ListOfLists.ExtractsAndRestores (0 ms)
10: [ RUN ] ListOfLists.AppendsListOfListsWithOffset
10: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms)
10: [----------] 9 tests from ListOfLists (1 ms total)
10:
10: [----------] 7 tests from LoggerTest
10: [ RUN ] LoggerTest.EmptyLoggerWorks
10: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
10: [ RUN ] LoggerTest.LogsToStream
10: [ OK ] LoggerTest.LogsToStream (1 ms)
10: [ RUN ] LoggerTest.LogsToFile
10: [ OK ] LoggerTest.LogsToFile (0 ms)
10: [ RUN ] LoggerTest.LevelFilteringWorks
10: [ OK ] LoggerTest.LevelFilteringWorks (1 ms)
10: [ RUN ] LoggerTest.LogsToMultipleStreams
10: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
10: [ RUN ] LoggerTest.LogsToMultipleFiles
10: [ OK ] LoggerTest.LogsToMultipleFiles (2 ms)
10: [ RUN ] LoggerTest.LogsToStreamAndFile
10: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms)
10: [----------] 7 tests from LoggerTest (5 ms total)
10:
10: [----------] 4 tests from MDModuleNotificationTest
10: [ RUN ] MDModuleNotificationTest.addConsumer
10: [ OK ] MDModuleNotificationTest.addConsumer (0 ms)
10: [ RUN ] MDModuleNotificationTest.addConsumerWithPointerParameter
10: [ OK ] MDModuleNotificationTest.addConsumerWithPointerParameter (0 ms)
10: [ RUN ] MDModuleNotificationTest.addTwoDifferentConsumers
10: [ OK ] MDModuleNotificationTest.addTwoDifferentConsumers (0 ms)
10: [ RUN ] MDModuleNotificationTest.consumerOfTwoResources
10: [ OK ] MDModuleNotificationTest.consumerOfTwoResources (0 ms)
10: [----------] 4 tests from MDModuleNotificationTest (0 ms total)
10:
10: [----------] 4 tests from MutexBasicTest
10: [ RUN ] MutexBasicTest.CanBeMade
10: [ OK ] MutexBasicTest.CanBeMade (0 ms)
10: [ RUN ] MutexBasicTest.CanBeLocked
10: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
10: [ RUN ] MutexBasicTest.CanBeTryLocked
10: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
10: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
10: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
10: [----------] 4 tests from MutexBasicTest (0 ms total)
10:
10: [----------] 3 tests from MutexTaskTest
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms)
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
10: [----------] 3 tests from MutexTaskTest (0 ms total)
10:
10: [----------] 2 tests from PathTest
10: [ RUN ] PathTest.StripSourcePrefixWorks
10: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
10: [ RUN ] PathTest.SearchOperationsWork
10: [ OK ] PathTest.SearchOperationsWork (11 ms)
10: [----------] 2 tests from PathTest (11 ms total)
10:
10: [----------] 2 tests from PhysicalNodeCommunicatorTest
10: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
10: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
10: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
10: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
10: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
10:
10: [----------] 5 tests from Range
10: [ RUN ] Range.EmptyRangeWorks
10: [ OK ] Range.EmptyRangeWorks (0 ms)
10: [ RUN ] Range.NonEmptyRangeWorks
10: [ OK ] Range.NonEmptyRangeWorks (0 ms)
10: [ RUN ] Range.BeginEnd
10: [ OK ] Range.BeginEnd (0 ms)
10: [ RUN ] Range.IsInRangeWorks
10: [ OK ] Range.IsInRangeWorks (0 ms)
10: [ RUN ] Range.IteratorWorks
10: [ OK ] Range.IteratorWorks (0 ms)
10: [----------] 5 tests from Range (0 ms total)
10:
10: [----------] 7 tests from StringConvert
10: [ RUN ] StringConvert.NoResultFromEptyString
10: [ OK ] StringConvert.NoResultFromEptyString (0 ms)
10: [ RUN ] StringConvert.ThreeFloatsSuccessfully
10: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms)
10: [ RUN ] StringConvert.OneIntSucessfully
10: [ OK ] StringConvert.OneIntSucessfully (0 ms)
10: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows
10: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms)
10: [ RUN ] StringConvert.ThrowsWhenWrongSize
10: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms)
10: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows
10: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms)
10: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay
10: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms)
10: [----------] 7 tests from StringConvert (0 ms total)
10:
10: [----------] 9 tests from StringUtilityTest
10: [ RUN ] StringUtilityTest.StartsWith
10: [ OK ] StringUtilityTest.StartsWith (0 ms)
10: [ RUN ] StringUtilityTest.EndsWith
10: [ OK ] StringUtilityTest.EndsWith (0 ms)
10: [ RUN ] StringUtilityTest.StripSuffixIfPresent
10: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
10: [ RUN ] StringUtilityTest.StripString
10: [ OK ] StringUtilityTest.StripString (0 ms)
10: [ RUN ] StringUtilityTest.SplitString
10: [ OK ] StringUtilityTest.SplitString (0 ms)
10: [ RUN ] StringUtilityTest.SplitDelimitedString
10: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms)
10: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
10: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
10: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
10: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
10: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
10: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
10: [----------] 9 tests from StringUtilityTest (2 ms total)
10:
10: [----------] 2 tests from FormatStringTest
10: [ RUN ] FormatStringTest.HandlesBasicFormatting
10: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
10: [ RUN ] FormatStringTest.HandlesLongStrings
10: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
10: [----------] 2 tests from FormatStringTest (0 ms total)
10:
10: [----------] 1 test from StringFormatterTest
10: [ RUN ] StringFormatterTest.HandlesBasicFormatting
10: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
10: [----------] 1 test from StringFormatterTest (0 ms total)
10:
10: [----------] 1 test from formatAndJoinTest
10: [ RUN ] formatAndJoinTest.Works
10: [ OK ] formatAndJoinTest.Works (0 ms)
10: [----------] 1 test from formatAndJoinTest (0 ms total)
10:
10: [----------] 1 test from JoinStringsTest
10: [ RUN ] JoinStringsTest.Works
10: [ OK ] JoinStringsTest.Works (0 ms)
10: [----------] 1 test from JoinStringsTest (0 ms total)
10:
10: [----------] 6 tests from ReplaceAllTest
10: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
10: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesNoMatches
10: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
10: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
10: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
10: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
10: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
10: [----------] 6 tests from ReplaceAllTest (0 ms total)
10:
10: [----------] 10 tests from TextLineWrapperTest
10: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
10: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
10: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
10: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectly
10: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
10: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesIndent
10: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
10: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (1 ms)
10: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
10: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
10: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
10: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
10: [----------] 10 tests from TextLineWrapperTest (2 ms total)
10:
10: [----------] 1 test from TemplateMPTest
10: [ RUN ] TemplateMPTest.DispatchTemplatedFunction
10: [ OK ] TemplateMPTest.DispatchTemplatedFunction (0 ms)
10: [----------] 1 test from TemplateMPTest (0 ms total)
10:
10: [----------] 6 tests from TextWriterTest
10: [ RUN ] TextWriterTest.WritesLines
10: [ OK ] TextWriterTest.WritesLines (1 ms)
10: [ RUN ] TextWriterTest.WritesLinesInParts
10: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
10: [ RUN ] TextWriterTest.WritesWrappedLines
10: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
10: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
10: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
10: [ RUN ] TextWriterTest.TracksNewlines
10: [ OK ] TextWriterTest.TracksNewlines (0 ms)
10: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
10: [ OK ] TextWriterTest.PreservesTrailingWhitespace (1 ms)
10: [----------] 6 tests from TextWriterTest (2 ms total)
10:
10: [----------] 1 test from TypeTraitsTest
10: [ RUN ] TypeTraitsTest.IsIntegralConstant
10: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
10: [----------] 1 test from TypeTraitsTest (0 ms total)
10:
10: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
10: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total)
10:
10: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
10: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total)
10:
10: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
10: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
10:
10: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (1 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
10: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total)
10:
10: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (1 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
10: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 373 tests from 61 test cases ran. (60 ms total)
10: [ PASSED ] 373 tests.
10/65 Test #10: UtilityUnitTests ...................... Passed 0.11 sec
test 11
Start 11: UtilityMpiUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 2 tests from 1 test case.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from PhysicalNodeCommunicatorTest
11: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
11: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (2 ms)
11: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
11: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms)
11: [----------] 2 tests from PhysicalNodeCommunicatorTest (3 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 2 tests from 1 test case ran. (3 ms total)
11: [ PASSED ] 2 tests.
11/65 Test #11: UtilityMpiUnitTests ................... Passed 0.04 sec
test 12
Start 12: MdlibUnitTest
12: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdlibUnitTest.xml"
12: Test timeout computed to be: 30
12: No protocol specified
12: [==========] Running 141 tests from 15 test cases.
12: [----------] Global test environment set-up.
12: [----------] 1 test from VerletBufferConstraintTest
12: [ RUN ] VerletBufferConstraintTest.EqualMasses
12: [ OK ] VerletBufferConstraintTest.EqualMasses (1 ms)
12: [----------] 1 test from VerletBufferConstraintTest (1 ms total)
12:
12: [----------] 2 tests from PrEbinTest
12: [ RUN ] PrEbinTest.HandlesAverages
12: [ OK ] PrEbinTest.HandlesAverages (7 ms)
12: [ RUN ] PrEbinTest.HandlesEmptyAverages
12: [ OK ] PrEbinTest.HandlesEmptyAverages (1 ms)
12: [----------] 2 tests from PrEbinTest (8 ms total)
12:
12: [----------] 3 tests from EnergyDriftTracker
12: [ RUN ] EnergyDriftTracker.emptyWorks
12: [ OK ] EnergyDriftTracker.emptyWorks (0 ms)
12: [ RUN ] EnergyDriftTracker.onePointWorks
12: [ OK ] EnergyDriftTracker.onePointWorks (0 ms)
12: [ RUN ] EnergyDriftTracker.manyPointsWorks
12: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms)
12: [----------] 3 tests from EnergyDriftTracker (0 ms total)
12:
12: [----------] 4 tests from ShakeTest
12: [ RUN ] ShakeTest.ConstrainsOneBond
12: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
12: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
12: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
12: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
12: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
12: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
12: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
12: [----------] 4 tests from ShakeTest (0 ms total)
12:
12: [----------] 1 test from NullSignalTest
12: [ RUN ] NullSignalTest.NullSignallerWorks
12: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
12: [----------] 1 test from NullSignalTest (0 ms total)
12:
12: [----------] 7 tests from SignalTest
12: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
12: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
12: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
12: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
12: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
12: [----------] 7 tests from SignalTest (0 ms total)
12:
12: [----------] 9 tests from UpdateGroups
12: [ RUN ] UpdateGroups.ethaneUA
12: [ OK ] UpdateGroups.ethaneUA (1 ms)
12: [ RUN ] UpdateGroups.methane
12: [ OK ] UpdateGroups.methane (0 ms)
12: [ RUN ] UpdateGroups.ethane
12: [ OK ] UpdateGroups.ethane (0 ms)
12: [ RUN ] UpdateGroups.butaneUA
12: [ OK ] UpdateGroups.butaneUA (0 ms)
12: [ RUN ] UpdateGroups.waterThreeSite
12: [ OK ] UpdateGroups.waterThreeSite (0 ms)
12: [ RUN ] UpdateGroups.waterFourSite
12: [ OK ] UpdateGroups.waterFourSite (0 ms)
12: [ RUN ] UpdateGroups.fourAtomsWithSettle
12: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
12: [ RUN ] UpdateGroups.waterFlexAngle
12: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
12: [ RUN ] UpdateGroups.twoMoltypes
12: [ OK ] UpdateGroups.twoMoltypes (0 ms)
12: [----------] 9 tests from UpdateGroups (1 ms total)
12:
12: [----------] 1 test from UpdateGroupsCog
12: [ RUN ] UpdateGroupsCog.ComputesCogs
12: [ OK ] UpdateGroupsCog.ComputesCogs (72 ms)
12: [----------] 1 test from UpdateGroupsCog (72 ms total)
12:
12: [----------] 12 tests from WithParameters/ConstraintsTest
12: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
12: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
12: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
12: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
12: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms)
12: [----------] 12 tests from WithParameters/ConstraintsTest (4 ms total)
12:
12: [----------] 11 tests from WithParameters/EnergyOutputTest
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (16 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (4 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (7 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
12: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (1 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file
12:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (27 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (8 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (9 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (10 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (9 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (7 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
12: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (7 ms)
12: [----------] 11 tests from WithParameters/EnergyOutputTest (118 ms total)
12:
12: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms)
12: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (4 ms total)
12:
12: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms)
12: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (2 ms total)
12:
12: [----------] 23 tests from WithParameters/FreeEnergyParameterTest
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms)
12: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (4 ms total)
12:
12: [----------] 16 tests from WithParameters/LeapFrogTest
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (6 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (16 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (39 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (14 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (14 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (6 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (6 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (6 ms)
12: [----------] 16 tests from WithParameters/LeapFrogTest (123 ms total)
12:
12: [----------] 13 tests from WithParameters/SettleTest
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (4 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (4 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (5 ms)
12: [----------] 13 tests from WithParameters/SettleTest (34 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 141 tests from 15 test cases ran. (372 ms total)
12: [ PASSED ] 141 tests.
12/65 Test #12: MdlibUnitTest ......................... Passed 0.87 sec
test 13
Start 13: AwhTest
13: Test command: /<<PKGBUILDDIR>>/build/basic/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AwhTest.xml"
13: Test timeout computed to be: 30
13: [==========] Running 17 tests from 6 test cases.
13: [----------] Global test environment set-up.
13: [----------] 1 test from BiasTest
13: [ RUN ] BiasTest.DetectsCovering
13: [ OK ] BiasTest.DetectsCovering (2 ms)
13: [----------] 1 test from BiasTest (2 ms total)
13:
13: [----------] 1 test from biasGridTest
13: [ RUN ] biasGridTest.neighborhood
13: [ OK ] biasGridTest.neighborhood (6 ms)
13: [----------] 1 test from biasGridTest (6 ms total)
13:
13: [----------] 1 test from BiasFepLambdaStateTest
13: [ RUN ] BiasFepLambdaStateTest.DetectsCovering
13: [ OK ] BiasFepLambdaStateTest.DetectsCovering (10 ms)
13: [----------] 1 test from BiasFepLambdaStateTest (10 ms total)
13:
13: [----------] 8 tests from WithParameters/BiasTest
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (16 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (2 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (2 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (2 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (2 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (2 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (2 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (2 ms)
13: [----------] 8 tests from WithParameters/BiasTest (32 ms total)
13:
13: [----------] 2 tests from WithParameters/BiasStateTest
13: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
13: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms)
13: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
13: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
13: [----------] 2 tests from WithParameters/BiasStateTest (3 ms total)
13:
13: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (22 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (22 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (23 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (23 ms)
13: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (95 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 17 tests from 6 test cases ran. (148 ms total)
13: [ PASSED ] 17 tests.
13/65 Test #13: AwhTest ............................... Passed 0.19 sec
test 14
Start 14: DensityFittingAppliedForcesUnitTest
14: Test command: /<<PKGBUILDDIR>>/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml"
14: Test timeout computed to be: 30
14: [==========] Running 18 tests from 4 test cases.
14: [----------] Global test environment set-up.
14: [----------] 2 tests from DensityFittingTest
14: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
14: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (1 ms)
14: [ RUN ] DensityFittingTest.SingleAtom
14: [ OK ] DensityFittingTest.SingleAtom (12 ms)
14: [----------] 2 tests from DensityFittingTest (14 ms total)
14:
14: [----------] 7 tests from DensityFittingAmplitudeLookupTest
14: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
14: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
14: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
14: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
14: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
14: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
14: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
14: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
14: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total)
14:
14: [----------] 1 test from DensityFittingForceProviderState
14: [ RUN ] DensityFittingForceProviderState.RoundTripSaving
14: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms)
14: [----------] 1 test from DensityFittingForceProviderState (0 ms total)
14:
14: [----------] 8 tests from DensityFittingOptionsTest
14: [ RUN ] DensityFittingOptionsTest.DefaultParameters
14: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
14: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
14: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms)
14: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
14: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms)
14: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
14: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms)
14: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
14: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms)
14: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
14: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
14: [ RUN ] DensityFittingOptionsTest.KvtToInternal
14: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms)
14: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
14: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms)
14: [----------] 8 tests from DensityFittingOptionsTest (2 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 18 tests from 4 test cases ran. (17 ms total)
14: [ PASSED ] 18 tests.
14/65 Test #14: DensityFittingAppliedForcesUnitTest ... Passed 0.05 sec
test 15
Start 15: AppliedForcesUnitTest
15: Test command: /<<PKGBUILDDIR>>/build/basic/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml"
15: Test timeout computed to be: 30
15: [==========] Running 3 tests from 1 test case.
15: [----------] Global test environment set-up.
15: [----------] 3 tests from ElectricFieldTest
15: [ RUN ] ElectricFieldTest.Static
15: [ OK ] ElectricFieldTest.Static (1 ms)
15: [ RUN ] ElectricFieldTest.Oscillating
15: [ OK ] ElectricFieldTest.Oscillating (0 ms)
15: [ RUN ] ElectricFieldTest.Pulsed
15: [ OK ] ElectricFieldTest.Pulsed (0 ms)
15: [----------] 3 tests from ElectricFieldTest (1 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 3 tests from 1 test case ran. (1 ms total)
15: [ PASSED ] 3 tests.
15/65 Test #15: AppliedForcesUnitTest ................. Passed 0.03 sec
test 16
Start 16: ListedForcesTest
16: Test command: /<<PKGBUILDDIR>>/build/basic/bin/listed_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ListedForcesTest.xml"
16: Test timeout computed to be: 30
16: [==========] Running 111 tests from 7 test cases.
16: [----------] Global test environment set-up.
16: [----------] 24 tests from Bond/ListedForcesTest
16: [ RUN ] Bond/ListedForcesTest.Ifunc/0
16: [ OK ] Bond/ListedForcesTest.Ifunc/0 (14 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/1
16: [ OK ] Bond/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/2
16: [ OK ] Bond/ListedForcesTest.Ifunc/2 (10 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/3
16: [ OK ] Bond/ListedForcesTest.Ifunc/3 (9 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/4
16: [ OK ] Bond/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/5
16: [ OK ] Bond/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/6
16: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/7
16: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/8
16: [ OK ] Bond/ListedForcesTest.Ifunc/8 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/9
16: [ OK ] Bond/ListedForcesTest.Ifunc/9 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/10
16: [ OK ] Bond/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/11
16: [ OK ] Bond/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/12
16: [ OK ] Bond/ListedForcesTest.Ifunc/12 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/13
16: [ OK ] Bond/ListedForcesTest.Ifunc/13 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/14
16: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/15
16: [ OK ] Bond/ListedForcesTest.Ifunc/15 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/16
16: [ OK ] Bond/ListedForcesTest.Ifunc/16 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/17
16: [ OK ] Bond/ListedForcesTest.Ifunc/17 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/18
16: [ OK ] Bond/ListedForcesTest.Ifunc/18 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/19
16: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/20
16: [ OK ] Bond/ListedForcesTest.Ifunc/20 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/21
16: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/22
16: [ OK ] Bond/ListedForcesTest.Ifunc/22 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/23
16: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms)
16: [----------] 24 tests from Bond/ListedForcesTest (51 ms total)
16:
16: [----------] 33 tests from Angle/ListedForcesTest
16: [ RUN ] Angle/ListedForcesTest.Ifunc/0
16: [ OK ] Angle/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/1
16: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/2
16: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/3
16: [ OK ] Angle/ListedForcesTest.Ifunc/3 (2 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/4
16: [ OK ] Angle/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/5
16: [ OK ] Angle/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/6
16: [ OK ] Angle/ListedForcesTest.Ifunc/6 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/7
16: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/8
16: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/9
16: [ OK ] Angle/ListedForcesTest.Ifunc/9 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/10
16: [ OK ] Angle/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/11
16: [ OK ] Angle/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/12
16: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/13
16: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/14
16: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/15
16: [ OK ] Angle/ListedForcesTest.Ifunc/15 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/16
16: [ OK ] Angle/ListedForcesTest.Ifunc/16 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/17
16: [ OK ] Angle/ListedForcesTest.Ifunc/17 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/18
16: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/19
16: [ OK ] Angle/ListedForcesTest.Ifunc/19 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/20
16: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/21
16: [ OK ] Angle/ListedForcesTest.Ifunc/21 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/22
16: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/23
16: [ OK ] Angle/ListedForcesTest.Ifunc/23 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/24
16: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/25
16: [ OK ] Angle/ListedForcesTest.Ifunc/25 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/26
16: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/27
16: [ OK ] Angle/ListedForcesTest.Ifunc/27 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/28
16: [ OK ] Angle/ListedForcesTest.Ifunc/28 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/29
16: [ OK ] Angle/ListedForcesTest.Ifunc/29 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/30
16: [ OK ] Angle/ListedForcesTest.Ifunc/30 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/31
16: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/32
16: [ OK ] Angle/ListedForcesTest.Ifunc/32 (1 ms)
16: [----------] 33 tests from Angle/ListedForcesTest (24 ms total)
16:
16: [----------] 18 tests from Dihedral/ListedForcesTest
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms)
16: [----------] 18 tests from Dihedral/ListedForcesTest (14 ms total)
16:
16: [----------] 12 tests from Polarize/ListedForcesTest
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/0
16: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/1
16: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/2
16: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/3
16: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/4
16: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/5
16: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/6
16: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/7
16: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/8
16: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/9
16: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/10
16: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/11
16: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms)
16: [----------] 12 tests from Polarize/ListedForcesTest (5 ms total)
16:
16: [----------] 18 tests from Restraints/ListedForcesTest
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/0
16: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/1
16: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/2
16: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/3
16: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/4
16: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/5
16: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/6
16: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/7
16: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/8
16: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/9
16: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/10
16: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/11
16: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/12
16: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/13
16: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/14
16: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/15
16: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (11 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/16
16: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (2 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/17
16: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (1 ms)
16: [----------] 18 tests from Restraints/ListedForcesTest (25 ms total)
16:
16: [----------] 3 tests from BondZeroLength/ListedForcesTest
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms)
16: [----------] 3 tests from BondZeroLength/ListedForcesTest (1 ms total)
16:
16: [----------] 3 tests from AngleZero/ListedForcesTest
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms)
16: [----------] 3 tests from AngleZero/ListedForcesTest (1 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 111 tests from 7 test cases ran. (122 ms total)
16: [ PASSED ] 111 tests.
16/65 Test #16: ListedForcesTest ...................... Passed 0.17 sec
test 17
Start 17: CommandLineUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CommandLineUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 59 tests from 7 test cases.
17: [----------] Global test environment set-up.
17: [----------] 3 tests from CommandLineHelpModuleTest
17: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
17: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (3 ms)
17: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
17: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
17: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
17: [ OK ] CommandLineHelpModuleTest.ExportsHelp (8 ms)
17: [----------] 3 tests from CommandLineHelpModuleTest (12 ms total)
17:
17: [----------] 7 tests from CommandLineHelpWriterTest
17: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
17: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (2 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
17: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
17: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
17: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
17: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
17: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
17: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (1 ms)
17: [----------] 7 tests from CommandLineHelpWriterTest (7 ms total)
17:
17: [----------] 6 tests from CommandLineModuleManagerTest
17: [ RUN ] CommandLineModuleManagerTest.RunsModule
17: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
17: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (1 ms)
17: [----------] 6 tests from CommandLineModuleManagerTest (4 ms total)
17:
17: [----------] 13 tests from CommandLineParserTest
17: [ RUN ] CommandLineParserTest.HandlesSingleValues
17: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
17: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (1 ms)
17: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
17: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
17: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
17: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
17: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (1 ms)
17: [ RUN ] CommandLineParserTest.HandlesString
17: [ OK ] CommandLineParserTest.HandlesString (0 ms)
17: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
17: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
17: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
17: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
17: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
17: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
17: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
17: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
17: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
17: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
17: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (1 ms)
17: [----------] 13 tests from CommandLineParserTest (4 ms total)
17:
17: [----------] 6 tests from CommandLineProgramContextTest
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (1 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
17: [----------] 6 tests from CommandLineProgramContextTest (2 ms total)
17:
17: [----------] 3 tests from OutputNamesTest
17: [ RUN ] OutputNamesTest.CanBeSuffixed
17: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
17: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
17: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
17: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
17: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
17: [----------] 3 tests from OutputNamesTest (0 ms total)
17:
17: [----------] 21 tests from ParseCommonArgsTest
17: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
17: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
17: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
17: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
17: [ OK ] ParseCommonArgsTest.ParsesStringArgs (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
17: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
17: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
17: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
17: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
17: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
17: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
17: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
17: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
17: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
17: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
17: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms)
17: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
17: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
17: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (1 ms)
17: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
17: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms)
17: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
17: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (2 ms)
17: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
17: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms)
17: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
17: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (1 ms)
17: [----------] 21 tests from ParseCommonArgsTest (11 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 59 tests from 7 test cases ran. (42 ms total)
17: [ PASSED ] 59 tests.
17/65 Test #17: CommandLineUnitTests .................. Passed 0.07 sec
test 18
Start 18: DomDecTests
18: Test command: /<<PKGBUILDDIR>>/build/basic/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DomDecTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 9 tests from 2 test cases.
18: [----------] Global test environment set-up.
18: [----------] 7 tests from HashedMap
18: [ RUN ] HashedMap.InsertsFinds
18: [ OK ] HashedMap.InsertsFinds (0 ms)
18: [ RUN ] HashedMap.NegativeKeysWork
18: [ OK ] HashedMap.NegativeKeysWork (0 ms)
18: [ RUN ] HashedMap.InsertsErases
18: [ OK ] HashedMap.InsertsErases (0 ms)
18: [ RUN ] HashedMap.InsertsOrAssigns
18: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
18: [ RUN ] HashedMap.Clears
18: [ OK ] HashedMap.Clears (0 ms)
18: [ RUN ] HashedMap.LinkedEntries
18: [ OK ] HashedMap.LinkedEntries (0 ms)
18: [ RUN ] HashedMap.ResizesTable
18: [ OK ] HashedMap.ResizesTable (0 ms)
18: [----------] 7 tests from HashedMap (0 ms total)
18:
18: [----------] 2 tests from LocalAtomSetManager
18: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
18: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
18: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
18: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
18: [----------] 2 tests from LocalAtomSetManager (1 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 9 tests from 2 test cases ran. (1 ms total)
18: [ PASSED ] 9 tests.
18/65 Test #18: DomDecTests ........................... Passed 0.03 sec
test 19
Start 19: DomDecMpiTests
19: Test command: /<<PKGBUILDDIR>>/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DomDecMpiTests.xml"
19: Test timeout computed to be: 30
19: No protocol specified
19: [==========] Running 4 tests from 1 test case.
19: [----------] Global test environment set-up.
19: [----------] 4 tests from HaloExchangeTest
19: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse
19: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (1 ms)
19: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses
19: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (9 ms)
19: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim
19: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (10 ms)
19: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1
19: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (10 ms)
19: [----------] 4 tests from HaloExchangeTest (30 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 4 tests from 1 test case ran. (30 ms total)
19: [ PASSED ] 4 tests.
19/65 Test #19: DomDecMpiTests ........................ Passed 0.08 sec
test 20
Start 20: EwaldUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EwaldUnitTests.xml"
20: Test timeout computed to be: 30
20: No protocol specified
20: [==========] Running 185 tests from 10 test cases.
20: [----------] Global test environment set-up.
20: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (10 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
20: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (11 ms total)
20:
20: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (116 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (12 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (11 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (7 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (7 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (13 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (7 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (9 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (10 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (10 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (10 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (10 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (30 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (11 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (10 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (8 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (8 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (8 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (8 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (9 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (8 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (8 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (10 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (16 ms)
20: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (363 ms total)
20:
20: [----------] 72 tests from SaneInput/PmeGatherTest
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (14 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (2 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms)
20: [----------] 72 tests from SaneInput/PmeGatherTest (106 ms total)
20:
20: [----------] 16 tests from SaneInput/PmeSolveTest
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (5 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (6 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (5 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (6 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (3 ms)
20: [----------] 16 tests from SaneInput/PmeSolveTest (58 ms total)
20:
20: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (3 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (3 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (3 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (2 ms)
20: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (19 ms total)
20:
20: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (5 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (4 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (3 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (4 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (5 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (3 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (3 ms)
20: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (31 ms total)
20:
20: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (4 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (1 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (1 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (4 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (3 ms)
20: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (38 ms total)
20:
20: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (12 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (6 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (4 ms)
20: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (58 ms total)
20:
20: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (3 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (4 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (5 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (6 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (3 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (5 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (6 ms)
20: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (57 ms total)
20:
20: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (8 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (9 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (16 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (17 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (16 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (18 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (8 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (8 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (11 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (23 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (21 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (23 ms)
20: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (190 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 185 tests from 10 test cases ran. (931 ms total)
20: [ PASSED ] 185 tests.
20/65 Test #20: EwaldUnitTests ........................ Passed 1.05 sec
test 21
Start 21: FFTUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FFTUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 14 tests from 4 test cases.
21: [----------] Global test environment set-up.
21: [----------] 2 tests from ManyFFTTest
21: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
21: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (19 ms)
21: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
21: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (28 ms)
21: [----------] 2 tests from ManyFFTTest (49 ms total)
21:
21: [----------] 1 test from FFTTest
21: [ RUN ] FFTTest.Real2DLength18_15Test
21: [ OK ] FFTTest.Real2DLength18_15Test (8 ms)
21: [----------] 1 test from FFTTest (9 ms total)
21:
21: [----------] 1 test from FFFTest3D
21: [ RUN ] FFFTest3D.Real5_6_9
21: [ OK ] FFFTest3D.Real5_6_9 (9 ms)
21: [----------] 1 test from FFFTest3D (10 ms total)
21:
21: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (13 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (3 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (6 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (4 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (2 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (17 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (25 ms)
21: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (74 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 14 tests from 4 test cases ran. (142 ms total)
21: [ PASSED ] 14 tests.
21/65 Test #21: FFTUnitTests .......................... Passed 0.18 sec
test 22
Start 22: GpuUtilsUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml"
22: Test timeout computed to be: 30
22: No protocol specified
22: [==========] Running 64 tests from 22 test cases.
22: [----------] Global test environment set-up.
22: [----------] 2 tests from ClfftInitializer
22: [ RUN ] ClfftInitializer.SingleInitializationWorks
22: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
22: [ RUN ] ClfftInitializer.TwoInitializationsWork
22: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
22: [----------] 2 tests from ClfftInitializer (0 ms total)
22:
22: [----------] 1 test from DevicesAvailable
22: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice
22: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms)
22: [----------] 1 test from DevicesAvailable (0 ms total)
22:
22: [----------] 1 test from DeviceStreamManagerTest
22: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice
22: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms)
22: [----------] 1 test from DeviceStreamManagerTest (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
22: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float
22: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<float>
22: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
22: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float
22: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<float>
22: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
22: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.Swap
22: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.Comparison
22: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float
22: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
22: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.Swap
22: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.Comparison
22: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<float>
22: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
22: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.Swap
22: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.Comparison
22: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
22: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
22: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.Swap
22: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.Comparison
22: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float
22: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (1 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<float>
22: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
22:
22: [----------] 1 test from HostAllocatorUntypedTest
22: [ RUN ] HostAllocatorUntypedTest.Comparison
22: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
22: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.Move
22: [ OK ] AllocatorTest/0.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/0 (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.Move
22: [ OK ] AllocatorTest/1.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/1 (1 ms total)
22:
22: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/2.Move
22: [ OK ] AllocatorTest/2.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/2 (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms)
22: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.Move
22: [ OK ] AllocatorTest/3.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/3 (1 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 64 tests from 22 test cases ran. (4 ms total)
22: [ PASSED ] 64 tests.
22/65 Test #22: GpuUtilsUnitTests ..................... Passed 0.08 sec
test 23
Start 23: HardwareUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/HardwareUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 6 tests from 3 test cases.
23: [----------] Global test environment set-up.
23: [----------] 1 test from CpuInfoTest
23: [ RUN ] CpuInfoTest.SupportLevel
23: [ OK ] CpuInfoTest.SupportLevel (1 ms)
23: [----------] 1 test from CpuInfoTest (1 ms total)
23:
23: [----------] 4 tests from HardwareTopologyTest
23: [ RUN ] HardwareTopologyTest.Execute
23: No protocol specified
23: [ OK ] HardwareTopologyTest.Execute (21 ms)
23: [ RUN ] HardwareTopologyTest.HwlocExecute
23: No protocol specified
23: [ OK ] HardwareTopologyTest.HwlocExecute (19 ms)
23: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
23: No protocol specified
23: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (20 ms)
23: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
23: No protocol specified
23: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (20 ms)
23: [----------] 4 tests from HardwareTopologyTest (80 ms total)
23:
23: [----------] 1 test from DevicesManagerTest
23: [ RUN ] DevicesManagerTest.Serialization
23: [ OK ] DevicesManagerTest.Serialization (0 ms)
23: [----------] 1 test from DevicesManagerTest (0 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 6 tests from 3 test cases ran. (81 ms total)
23: [ PASSED ] 6 tests.
23/65 Test #23: HardwareUnitTests ..................... Passed 0.11 sec
test 24
Start 24: MathUnitTests
24: Test command: /<<PKGBUILDDIR>>/build/basic/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MathUnitTests.xml"
24: Test timeout computed to be: 30
24: [==========] Running 292 tests from 32 test cases.
24: [----------] Global test environment set-up.
24: [----------] 1 test from EmptyArrayRefWithPaddingTest
24: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
24: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
24: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
24:
24: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
24: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
24: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
24: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
24: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
24: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
24: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
24:
24: [----------] 11 tests from TranslateAndScaleTest
24: [ RUN ] TranslateAndScaleTest.identityTransformation
24: [ OK ] TranslateAndScaleTest.identityTransformation (1 ms)
24: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
24: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
24: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
24: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
24: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
24: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector
24: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingIdentity
24: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
24: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector
24: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
24: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
24: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector
24: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms)
24: [----------] 11 tests from TranslateAndScaleTest (1 ms total)
24:
24: [----------] 2 tests from AffineTransformationTest
24: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors
24: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms)
24: [ RUN ] AffineTransformationTest.applyTransformationToVectors
24: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms)
24: [----------] 2 tests from AffineTransformationTest (0 ms total)
24:
24: [----------] 12 tests from DensitySimilarityTest
24: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
24: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
24: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
24: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms)
24: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
24: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
24: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
24: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
24: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
24: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
24: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (78 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
24: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (72 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
24: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (65 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
24: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (61 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
24: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (1 ms)
24: [----------] 12 tests from DensitySimilarityTest (278 ms total)
24:
24: [----------] 6 tests from StructureSimilarityTest
24: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
24: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
24: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
24: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
24: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
24: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
24: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
24: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
24: [----------] 6 tests from StructureSimilarityTest (0 ms total)
24:
24: [----------] 8 tests from ExponentialMovingAverage
24: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
24: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
24: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
24: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
24: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
24: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
24: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
24: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
24: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
24: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
24: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
24: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
24: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
24: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
24: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
24: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
24: [----------] 8 tests from ExponentialMovingAverage (0 ms total)
24:
24: [----------] 21 tests from FunctionTest
24: [ RUN ] FunctionTest.StaticLog2
24: [ OK ] FunctionTest.StaticLog2 (1 ms)
24: [ RUN ] FunctionTest.Log2I32Bit
24: [ OK ] FunctionTest.Log2I32Bit (0 ms)
24: [ RUN ] FunctionTest.Log2I64Bit
24: [ OK ] FunctionTest.Log2I64Bit (0 ms)
24: [ RUN ] FunctionTest.GreatestCommonDivisor
24: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
24: [ RUN ] FunctionTest.InvsqrtFloat
24: [ OK ] FunctionTest.InvsqrtFloat (1 ms)
24: [ RUN ] FunctionTest.InvsqrtDouble
24: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
24: [ RUN ] FunctionTest.InvsqrtInteger
24: [ OK ] FunctionTest.InvsqrtInteger (0 ms)
24: [ RUN ] FunctionTest.InvcbrtFloat
24: [ OK ] FunctionTest.InvcbrtFloat (1 ms)
24: [ RUN ] FunctionTest.InvcbrtDouble
24: [ OK ] FunctionTest.InvcbrtDouble (0 ms)
24: [ RUN ] FunctionTest.InvcbrtInteger
24: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
24: [ RUN ] FunctionTest.SixthrootFloat
24: [ OK ] FunctionTest.SixthrootFloat (0 ms)
24: [ RUN ] FunctionTest.SixthrootDouble
24: [ OK ] FunctionTest.SixthrootDouble (1 ms)
24: [ RUN ] FunctionTest.SixthrootInteger
24: [ OK ] FunctionTest.SixthrootInteger (0 ms)
24: [ RUN ] FunctionTest.InvsixthrootFloat
24: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
24: [ RUN ] FunctionTest.InvsixthrootDouble
24: [ OK ] FunctionTest.InvsixthrootDouble (0 ms)
24: [ RUN ] FunctionTest.InvsixthrootInteger
24: [ OK ] FunctionTest.InvsixthrootInteger (0 ms)
24: [ RUN ] FunctionTest.Powers
24: [ OK ] FunctionTest.Powers (0 ms)
24: [ RUN ] FunctionTest.ErfInvFloat
24: [ OK ] FunctionTest.ErfInvFloat (0 ms)
24: [ RUN ] FunctionTest.ErfInvDouble
24: [ OK ] FunctionTest.ErfInvDouble (0 ms)
24: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
24: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms)
24: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
24: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms)
24: [----------] 21 tests from FunctionTest (6 ms total)
24:
24: [----------] 4 tests from GaussianOn1DLattice
24: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
24: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
24: [ RUN ] GaussianOn1DLattice.isCorrect
24: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
24: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
24: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms)
24: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
24: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
24: [----------] 4 tests from GaussianOn1DLattice (1 ms total)
24:
24: [----------] 9 tests from GaussTransformTest
24: [ RUN ] GaussTransformTest.isZeroUponConstruction
24: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
24: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
24: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
24: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
24: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
24: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
24: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
24: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
24: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms)
24: [ RUN ] GaussTransformTest.view
24: [ OK ] GaussTransformTest.view (0 ms)
24: [----------] 9 tests from GaussTransformTest (0 ms total)
24:
24: [----------] 3 tests from DensityFittingForce
24: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
24: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
24: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
24: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
24: [ RUN ] DensityFittingForce.pullsTowardsDerivative
24: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
24: [----------] 3 tests from DensityFittingForce (0 ms total)
24:
24: [----------] 2 tests from InvertMatrixTest
24: [ RUN ] InvertMatrixTest.IdentityIsImpotent
24: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
24: [ RUN ] InvertMatrixTest.ComputesInverse
24: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
24: [----------] 2 tests from InvertMatrixTest (0 ms total)
24:
24: [----------] 2 tests from InvertBoxMatrixTest
24: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
24: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
24: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
24: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
24: [----------] 2 tests from InvertBoxMatrixTest (1 ms total)
24:
24: [----------] 17 tests from MatrixTest
24: [ RUN ] MatrixTest.canSetFromArray
24: [ OK ] MatrixTest.canSetFromArray (0 ms)
24: [ RUN ] MatrixTest.canSetStaticallyFromList
24: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
24: [ RUN ] MatrixTest.canConstructAndFill
24: [ OK ] MatrixTest.canConstructAndFill (0 ms)
24: [ RUN ] MatrixTest.canSetValues
24: [ OK ] MatrixTest.canSetValues (0 ms)
24: [ RUN ] MatrixTest.canCopyAssign
24: [ OK ] MatrixTest.canCopyAssign (0 ms)
24: [ RUN ] MatrixTest.canSwap
24: [ OK ] MatrixTest.canSwap (0 ms)
24: [ RUN ] MatrixTest.staticMultiDimArrayExtent
24: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
24: [ RUN ] MatrixTest.determinantWorks
24: [ OK ] MatrixTest.determinantWorks (0 ms)
24: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
24: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
24: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
24: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
24: [ RUN ] MatrixTest.traceWorks
24: [ OK ] MatrixTest.traceWorks (0 ms)
24: [ RUN ] MatrixTest.transposeWorks
24: [ OK ] MatrixTest.transposeWorks (0 ms)
24: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
24: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
24: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
24: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
24: [ RUN ] MatrixTest.canFillLegacyMatrix
24: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
24: [ RUN ] MatrixTest.IdentityMatrix
24: [ OK ] MatrixTest.IdentityMatrix (0 ms)
24: [ RUN ] MatrixTest.MatrixVectorMultiplication
24: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms)
24: [----------] 17 tests from MatrixTest (0 ms total)
24:
24: [----------] 25 tests from MultiDimArrayTest
24: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
24: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
24: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
24: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
24: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
24: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
24: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
24: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
24: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
24: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
24: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
24: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
24: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSwapStatic
24: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSwapDynamic
24: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
24: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
24: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
24: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
24: [ RUN ] MultiDimArrayTest.conversionToView
24: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
24: [ RUN ] MultiDimArrayTest.conversionToConstView
24: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
24: [ RUN ] MultiDimArrayTest.viewBegin
24: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
24: [ RUN ] MultiDimArrayTest.viewEnd
24: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
24: [ RUN ] MultiDimArrayTest.constViewConstBegin
24: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
24: [ RUN ] MultiDimArrayTest.constViewConstEnd
24: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
24: [----------] 25 tests from MultiDimArrayTest (1 ms total)
24:
24: [----------] 4 tests from MultiDimArrayToMdSpanTest
24: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
24: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
24:
24: [----------] 9 tests from NelderMeadSimplexTest
24: [ RUN ] NelderMeadSimplexTest.BestVertex
24: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms)
24: [ RUN ] NelderMeadSimplexTest.WorstVertex
24: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms)
24: [ RUN ] NelderMeadSimplexTest.SecondWorstValue
24: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms)
24: [ RUN ] NelderMeadSimplexTest.ReflectionPoint
24: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint
24: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint
24: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.SwapOutWorst
24: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms)
24: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest
24: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms)
24: [ RUN ] NelderMeadSimplexTest.OrientedLength
24: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms)
24: [----------] 9 tests from NelderMeadSimplexTest (0 ms total)
24:
24: [----------] 2 tests from NelderMead
24: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly
24: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (1 ms)
24: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly
24: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms)
24: [----------] 2 tests from NelderMead (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
24: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ResizeWorks
24: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ReserveWorks
24: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanCopyAssign
24: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanMoveAssign
24: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanSwap
24: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/0 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
24: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ResizeWorks
24: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ReserveWorks
24: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanCopyAssign
24: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanMoveAssign
24: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanSwap
24: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/1 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
24: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ResizeWorks
24: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ReserveWorks
24: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanCopyAssign
24: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanMoveAssign
24: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanSwap
24: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/2 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
24: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ResizeWorks
24: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ReserveWorks
24: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanCopyAssign
24: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanMoveAssign
24: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanSwap
24: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/3 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
24: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ResizeWorks
24: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ReserveWorks
24: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanCopyAssign
24: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanMoveAssign
24: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanSwap
24: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/4 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ResizeWorks
24: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ReserveWorks
24: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanCopyAssign
24: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanMoveAssign
24: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanSwap
24: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/5 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ResizeWorks
24: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ReserveWorks
24: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanCopyAssign
24: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanMoveAssign
24: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanSwap
24: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/6 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ResizeWorks
24: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ReserveWorks
24: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanCopyAssign
24: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanMoveAssign
24: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanSwap
24: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/7 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ResizeWorks
24: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ReserveWorks
24: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (1 ms)
24: [ RUN ] PaddedVectorTest/8.CanCopyAssign
24: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanMoveAssign
24: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanSwap
24: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/8 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ResizeWorks
24: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ReserveWorks
24: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanCopyAssign
24: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanMoveAssign
24: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanSwap
24: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/9 (0 ms total)
24:
24: [----------] 37 tests from RVecTest
24: [ RUN ] RVecTest.CanBeStoredInVector
24: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
24: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
24: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
24: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
24: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
24: [ RUN ] RVecTest.WorksAsMutable_rvec
24: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
24: [ RUN ] RVecTest.WorksAs_rvec_Array
24: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
24: [ RUN ] RVecTest.CanAddRVecToRvec
24: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
24: [ RUN ] RVecTest.CanAddAssignRVecToRvec
24: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
24: [ RUN ] RVecTest.CanSubtractRVecFromRvec
24: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
24: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
24: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
24: [ RUN ] RVecTest.CanDotProductRVecByRvec
24: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
24: [ RUN ] RVecTest.CanCrossProductRVecByRvec
24: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
24: [ RUN ] RVecTest.CanDivideRVecInplace
24: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
24: [ RUN ] RVecTest.CanScaleRVec
24: [ OK ] RVecTest.CanScaleRVec (0 ms)
24: [ RUN ] RVecTest.CanDivideRVec
24: [ OK ] RVecTest.CanDivideRVec (0 ms)
24: [ RUN ] RVecTest.CanDoUnitvFromRVec
24: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
24: [ RUN ] RVecTest.CanSqLengthOfRVec
24: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanLengthOfRVec
24: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanCastToRVec
24: [ OK ] RVecTest.CanCastToRVec (0 ms)
24: [ RUN ] RVecTest.CanCastToDVec
24: [ OK ] RVecTest.CanCastToDVec (0 ms)
24: [ RUN ] RVecTest.CanLeftScalarMultiply
24: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
24: [ RUN ] RVecTest.CanRightScalarMultiply
24: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
24: [ RUN ] RVecTest.CanGetUnitvFromRVec
24: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
24: [ RUN ] RVecTest.CanGetSqLengthOfRVec
24: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanGetLengthOfRVec
24: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanDoCrossProductOfRVec
24: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
24: [ RUN ] RVecTest.CanDoDotProductOfRVec
24: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
24: [ RUN ] RVecTest.CanScaleByVector
24: [ OK ] RVecTest.CanScaleByVector (0 ms)
24: [ RUN ] RVecTest.asIVec
24: [ OK ] RVecTest.asIVec (0 ms)
24: [ RUN ] RVecTest.elementWiseMin
24: [ OK ] RVecTest.elementWiseMin (0 ms)
24: [ RUN ] RVecTest.elementWiseMax
24: [ OK ] RVecTest.elementWiseMax (0 ms)
24: [ RUN ] RVecTest.WorksAs_dvec_Reference
24: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
24: [ RUN ] RVecTest.WorksAs_ivec_Reference
24: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
24: [ RUN ] RVecTest.WorksAs_rvec_Reference
24: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
24: [ RUN ] RVecTest.CopyConstructorWorks
24: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
24: [ RUN ] RVecTest.CopyAssignmentWorks
24: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
24: [ RUN ] RVecTest.MoveConstructorWorks
24: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
24: [ RUN ] RVecTest.MoveAssignmentWorks
24: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
24: [----------] 37 tests from RVecTest (1 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 292 tests from 32 test cases ran. (294 ms total)
24: [ PASSED ] 292 tests.
24/65 Test #24: MathUnitTests ......................... Passed 0.34 sec
test 25
Start 25: MdrunUtilityUnitTests
25: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml"
25: Test timeout computed to be: 30
25: [==========] Running 17 tests from 1 test case.
25: [----------] Global test environment set-up.
25: [----------] 17 tests from ThreadAffinityTest
25: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
25: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
25: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
25: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms)
25: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
25: NOTE: Affinity setting failed.
25: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms)
25: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
25: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
25: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
25: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
25: NOTE: Affinity setting for 1/2 threads failed.
25: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms)
25: [----------] 17 tests from ThreadAffinityTest (8 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 17 tests from 1 test case ran. (8 ms total)
25: [ PASSED ] 17 tests.
25/65 Test #25: MdrunUtilityUnitTests ................. Passed 0.04 sec
test 26
Start 26: MdrunUtilityMpiUnitTests
26: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
26: Test timeout computed to be: 30
26: [==========] Running 13 tests from 2 test cases.
26: [----------] Global test environment set-up.
26: [----------] 6 tests from ThreadAffinityMultiRankTest
26: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
26: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (3 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
26: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (16 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
26: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (2 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
26: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (1 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
26: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (2 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
26: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (1 ms)
26: [----------] 6 tests from ThreadAffinityMultiRankTest (26 ms total)
26:
26: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (2 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (2 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (2 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (2 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (2 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (2 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (2 ms)
26: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (15 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 13 tests from 2 test cases ran. (44 ms total)
26: [ PASSED ] 13 tests.
26/65 Test #26: MdrunUtilityMpiUnitTests .............. Passed 0.08 sec
test 27
Start 27: MDSpanTests
27: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MDSpanTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 32 tests from 7 test cases.
27: [----------] Global test environment set-up.
27: [----------] 4 tests from BasicAccessorPolicy
27: [ RUN ] BasicAccessorPolicy.Decay
27: [ OK ] BasicAccessorPolicy.Decay (0 ms)
27: [ RUN ] BasicAccessorPolicy.Access
27: [ OK ] BasicAccessorPolicy.Access (0 ms)
27: [ RUN ] BasicAccessorPolicy.Offset
27: [ OK ] BasicAccessorPolicy.Offset (0 ms)
27: [ RUN ] BasicAccessorPolicy.CopyAccessor
27: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
27: [----------] 4 tests from BasicAccessorPolicy (0 ms total)
27:
27: [----------] 4 tests from ExtentsTest
27: [ RUN ] ExtentsTest.Construction
27: [ OK ] ExtentsTest.Construction (0 ms)
27: [ RUN ] ExtentsTest.PurelyStatic
27: [ OK ] ExtentsTest.PurelyStatic (0 ms)
27: [ RUN ] ExtentsTest.RankNought
27: [ OK ] ExtentsTest.RankNought (0 ms)
27: [ RUN ] ExtentsTest.Assignment
27: [ OK ] ExtentsTest.Assignment (0 ms)
27: [----------] 4 tests from ExtentsTest (0 ms total)
27:
27: [----------] 8 tests from MdSpanExtension
27: [ RUN ] MdSpanExtension.SlicingAllStatic
27: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
27: [ RUN ] MdSpanExtension.SlicingDynamic
27: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
27: [ RUN ] MdSpanExtension.SlicingAllStatic3D
27: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
27: [ RUN ] MdSpanExtension.SlicingEqualsView3D
27: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
27: [ RUN ] MdSpanExtension.additionWorks
27: [ OK ] MdSpanExtension.additionWorks (0 ms)
27: [ RUN ] MdSpanExtension.subtractionWorks
27: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
27: [ RUN ] MdSpanExtension.multiplicationWorks
27: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
27: [ RUN ] MdSpanExtension.divisionWorks
27: [ OK ] MdSpanExtension.divisionWorks (0 ms)
27: [----------] 8 tests from MdSpanExtension (0 ms total)
27:
27: [----------] 3 tests from LayoutTests
27: [ RUN ] LayoutTests.LayoutRightConstruction
27: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
27: [ RUN ] LayoutTests.LayoutRightProperties
27: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
27: [ RUN ] LayoutTests.LayoutRightOperator
27: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
27: [----------] 3 tests from LayoutTests (1 ms total)
27:
27: [----------] 1 test from MdSpanTest
27: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
27: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
27: [----------] 1 test from MdSpanTest (0 ms total)
27:
27: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
27: [ RUN ] MdSpanTest/0.Rank
27: [ OK ] MdSpanTest/0.Rank (0 ms)
27: [ RUN ] MdSpanTest/0.DynamicRank
27: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
27: [ RUN ] MdSpanTest/0.Extents
27: [ OK ] MdSpanTest/0.Extents (0 ms)
27: [ RUN ] MdSpanTest/0.Strides
27: [ OK ] MdSpanTest/0.Strides (0 ms)
27: [ RUN ] MdSpanTest/0.Properties
27: [ OK ] MdSpanTest/0.Properties (0 ms)
27: [ RUN ] MdSpanTest/0.Operator
27: [ OK ] MdSpanTest/0.Operator (0 ms)
27: [----------] 6 tests from MdSpanTest/0 (0 ms total)
27:
27: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
27: [ RUN ] MdSpanTest/1.Rank
27: [ OK ] MdSpanTest/1.Rank (0 ms)
27: [ RUN ] MdSpanTest/1.DynamicRank
27: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
27: [ RUN ] MdSpanTest/1.Extents
27: [ OK ] MdSpanTest/1.Extents (0 ms)
27: [ RUN ] MdSpanTest/1.Strides
27: [ OK ] MdSpanTest/1.Strides (0 ms)
27: [ RUN ] MdSpanTest/1.Properties
27: [ OK ] MdSpanTest/1.Properties (0 ms)
27: [ RUN ] MdSpanTest/1.Operator
27: [ OK ] MdSpanTest/1.Operator (0 ms)
27: [----------] 6 tests from MdSpanTest/1 (0 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 32 tests from 7 test cases ran. (1 ms total)
27: [ PASSED ] 32 tests.
27/65 Test #27: MDSpanTests ........................... Passed 0.04 sec
test 28
Start 28: MdtypesUnitTest
28: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdtypes-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdtypesUnitTest.xml"
28: Test timeout computed to be: 30
28: [==========] Running 9 tests from 2 test cases.
28: [----------] Global test environment set-up.
28: [----------] 2 tests from CheckpointDataTest
28: [ RUN ] CheckpointDataTest.SingleDataTest
28: [ OK ] CheckpointDataTest.SingleDataTest (7 ms)
28: [ RUN ] CheckpointDataTest.MultiDataTest
28: [ OK ] CheckpointDataTest.MultiDataTest (32 ms)
28: [----------] 2 tests from CheckpointDataTest (39 ms total)
28:
28: [----------] 7 tests from ForceBuffers
28: [ RUN ] ForceBuffers.ConstructsUnpinned
28: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms)
28: [ RUN ] ForceBuffers.ConstructsPinned
28: [ OK ] ForceBuffers.ConstructsPinned (0 ms)
28: [ RUN ] ForceBuffers.ConstructsEmpty
28: [ OK ] ForceBuffers.ConstructsEmpty (0 ms)
28: [ RUN ] ForceBuffers.ResizeWorks
28: [ OK ] ForceBuffers.ResizeWorks (1 ms)
28: [ RUN ] ForceBuffers.PaddingWorks
28: [ OK ] ForceBuffers.PaddingWorks (0 ms)
28: [ RUN ] ForceBuffers.CopyWorks
28: [ OK ] ForceBuffers.CopyWorks (0 ms)
28: [ RUN ] ForceBuffers.CopyDoesNotPin
28: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms)
28: [----------] 7 tests from ForceBuffers (1 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 9 tests from 2 test cases ran. (40 ms total)
28: [ PASSED ] 9 tests.
28/65 Test #28: MdtypesUnitTest ....................... Passed 0.08 sec
test 29
Start 29: OnlineHelpUnitTests
29: Test command: /<<PKGBUILDDIR>>/build/basic/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml"
29: Test timeout computed to be: 30
29: [==========] Running 22 tests from 4 test cases.
29: [----------] Global test environment set-up.
29: [----------] 6 tests from TextTableFormatterTest
29: [ RUN ] TextTableFormatterTest.HandlesBasicCase
29: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
29: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesIndentation
29: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
29: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
29: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
29: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
29: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (1 ms)
29: [----------] 6 tests from TextTableFormatterTest (2 ms total)
29:
29: [----------] 3 tests from HelpManagerTest
29: [ RUN ] HelpManagerTest.HandlesRootTopic
29: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms)
29: [ RUN ] HelpManagerTest.HandlesSubTopics
29: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
29: [ RUN ] HelpManagerTest.HandlesInvalidTopics
29: [ OK ] HelpManagerTest.HandlesInvalidTopics (1 ms)
29: [----------] 3 tests from HelpManagerTest (1 ms total)
29:
29: [----------] 2 tests from HelpTopicFormattingTest
29: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
29: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms)
29: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
29: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
29: [----------] 2 tests from HelpTopicFormattingTest (1 ms total)
29:
29: [----------] 11 tests from HelpWriterContextTest
29: [ RUN ] HelpWriterContextTest.FormatsParagraphs
29: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
29: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms)
29: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
29: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralText
29: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
29: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
29: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsBulletList
29: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
29: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
29: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsGridTable
29: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsTitles
29: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
29: [----------] 11 tests from HelpWriterContextTest (3 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 22 tests from 4 test cases ran. (8 ms total)
29: [ PASSED ] 22 tests.
29/65 Test #29: OnlineHelpUnitTests ................... Passed 0.04 sec
test 30
Start 30: OptionsUnitTests
30: Test command: /<<PKGBUILDDIR>>/build/basic/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OptionsUnitTests.xml"
30: Test timeout computed to be: 30
30: [==========] Running 111 tests from 18 test cases.
30: [----------] Global test environment set-up.
30: [----------] 5 tests from AbstractOptionStorageTest
30: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
30: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
30: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
30: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
30: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms)
30: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
30: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms)
30: [----------] 5 tests from AbstractOptionStorageTest (1 ms total)
30:
30: [----------] 10 tests from FileNameOptionTest
30: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (1 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
30: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
30: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
30: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
30: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
30: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
30: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue
30: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms)
30: [----------] 10 tests from FileNameOptionTest (1 ms total)
30:
30: [----------] 15 tests from FileNameOptionManagerTest
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
30: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (1 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
30: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
30: [----------] 15 tests from FileNameOptionManagerTest (1 ms total)
30:
30: [----------] 1 test from OptionsTest
30: [ RUN ] OptionsTest.FailsOnNonsafeStorage
30: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
30: [----------] 1 test from OptionsTest (1 ms total)
30:
30: [----------] 9 tests from OptionsAssignerTest
30: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
30: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
30: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
30: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
30: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMissingValue
30: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesExtraValue
30: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesGroups
30: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesSections
30: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
30: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
30: [----------] 9 tests from OptionsAssignerTest (0 ms total)
30:
30: [----------] 4 tests from OptionsAssignerBooleanTest
30: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
30: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
30: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
30: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
30: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (1 ms)
30: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
30:
30: [----------] 13 tests from OptionsAssignerIntegerTest
30: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
30: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
30: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
30: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
30: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
30: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
30: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
30: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
30: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total)
30:
30: [----------] 5 tests from OptionsAssignerDoubleTest
30: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
30: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
30: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (1 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
30: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total)
30:
30: [----------] 9 tests from OptionsAssignerStringTest
30: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
30: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
30: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
30: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
30: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
30: [----------] 9 tests from OptionsAssignerStringTest (0 ms total)
30:
30: [----------] 6 tests from OptionsAssignerEnumTest
30: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
30: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
30: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
30: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
30: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total)
30:
30: [----------] 8 tests from RepeatingOptionSectionTest
30: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
30: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
30: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
30: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
30: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
30: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (1 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
30: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
30: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
30: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
30: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total)
30:
30: [----------] 1 test from TimeUnitManagerTest
30: [ RUN ] TimeUnitManagerTest.BasicOperations
30: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
30: [----------] 1 test from TimeUnitManagerTest (0 ms total)
30:
30: [----------] 4 tests from TimeUnitBehaviorTest
30: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
30: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
30: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
30: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
30: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
30: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total)
30:
30: [----------] 2 tests from TreeValueSupportAssignTest
30: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
30: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
30: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
30: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
30: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
30:
30: [----------] 1 test from TreeValueSupportAssignErrorTest
30: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
30: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
30: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
30:
30: [----------] 5 tests from TreeValueSupportCheckTest
30: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
30: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
30: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
30: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
30: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
30: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
30: [----------] 5 tests from TreeValueSupportCheckTest (1 ms total)
30:
30: [----------] 6 tests from TreeValueSupportAdjustTest
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (1 ms)
30: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
30: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
30: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
30: [ OK ] TreeValueSupportAdjustTest.OrdersValues (1 ms)
30: [----------] 6 tests from TreeValueSupportAdjustTest (2 ms total)
30:
30: [----------] 7 tests from TreeValueSupportTest
30: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
30: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
30: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsInt64Option
30: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsStringOption
30: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsFloatOption
30: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
30: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsEnumOption
30: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms)
30: [----------] 7 tests from TreeValueSupportTest (2 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 111 tests from 18 test cases ran. (12 ms total)
30: [ PASSED ] 111 tests.
30/65 Test #30: OptionsUnitTests ...................... Passed 0.05 sec
test 31
Start 31: PbcutilUnitTest
31: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PbcutilUnitTest.xml"
31: Test timeout computed to be: 30
31: [==========] Running 33 tests from 5 test cases.
31: [----------] Global test environment set-up.
31: [----------] 1 test from ShiftTest
31: [ RUN ] ShiftTest.CoordinateShiftWorks
31: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms)
31: [----------] 1 test from ShiftTest (0 ms total)
31:
31: [----------] 2 tests from MShift
31: [ RUN ] MShift.shiftsAndUnshifts
31: [ OK ] MShift.shiftsAndUnshifts (1 ms)
31: [ RUN ] MShift.shiftsAndUnshiftsSelf
31: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms)
31: [----------] 2 tests from MShift (1 ms total)
31:
31: [----------] 1 test from PbcTest
31: [ RUN ] PbcTest.CalcShiftsWorks
31: [ OK ] PbcTest.CalcShiftsWorks (56 ms)
31: [----------] 1 test from PbcTest (56 ms total)
31:
31: [----------] 2 tests from PbcEnumsTest
31: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
31: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
31: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
31: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
31: [----------] 2 tests from PbcEnumsTest (0 ms total)
31:
31: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (6 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (9 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (1 ms)
31: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (41 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 33 tests from 5 test cases ran. (98 ms total)
31: [ PASSED ] 33 tests.
31/65 Test #31: PbcutilUnitTest ....................... Passed 0.13 sec
test 32
Start 32: RandomUnitTests
32: Test command: /<<PKGBUILDDIR>>/build/basic/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RandomUnitTests.xml"
32: Test timeout computed to be: 30
32: [==========] Running 44 tests from 10 test cases.
32: [----------] Global test environment set-up.
32: [----------] 4 tests from ExponentialDistributionTest
32: [ RUN ] ExponentialDistributionTest.Output
32: [ OK ] ExponentialDistributionTest.Output (1 ms)
32: [ RUN ] ExponentialDistributionTest.Logical
32: [ OK ] ExponentialDistributionTest.Logical (0 ms)
32: [ RUN ] ExponentialDistributionTest.Reset
32: [ OK ] ExponentialDistributionTest.Reset (0 ms)
32: [ RUN ] ExponentialDistributionTest.AltParam
32: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from ExponentialDistributionTest (1 ms total)
32:
32: [----------] 4 tests from GammaDistributionTest
32: [ RUN ] GammaDistributionTest.Output
32: [ OK ] GammaDistributionTest.Output (0 ms)
32: [ RUN ] GammaDistributionTest.Logical
32: [ OK ] GammaDistributionTest.Logical (0 ms)
32: [ RUN ] GammaDistributionTest.Reset
32: [ OK ] GammaDistributionTest.Reset (0 ms)
32: [ RUN ] GammaDistributionTest.AltParam
32: [ OK ] GammaDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from GammaDistributionTest (0 ms total)
32:
32: [----------] 4 tests from NormalDistributionTest
32: [ RUN ] NormalDistributionTest.Output
32: [ OK ] NormalDistributionTest.Output (1 ms)
32: [ RUN ] NormalDistributionTest.Logical
32: [ OK ] NormalDistributionTest.Logical (0 ms)
32: [ RUN ] NormalDistributionTest.Reset
32: [ OK ] NormalDistributionTest.Reset (0 ms)
32: [ RUN ] NormalDistributionTest.AltParam
32: [ OK ] NormalDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from NormalDistributionTest (1 ms total)
32:
32: [----------] 1 test from SeedTest
32: [ RUN ] SeedTest.makeRandomSeed
32: [ OK ] SeedTest.makeRandomSeed (0 ms)
32: [----------] 1 test from SeedTest (0 ms total)
32:
32: [----------] 6 tests from TabulatedNormalDistributionTest
32: [ RUN ] TabulatedNormalDistributionTest.Output14
32: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Output16
32: [ OK ] TabulatedNormalDistributionTest.Output16 (1 ms)
32: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
32: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Logical
32: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Reset
32: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.AltParam
32: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
32: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total)
32:
32: [----------] 1 test from TabulatedNormalDistributionTableTest
32: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
32: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (3 ms)
32: [----------] 1 test from TabulatedNormalDistributionTableTest (3 ms total)
32:
32: [----------] 6 tests from ThreeFry2x64Test
32: [ RUN ] ThreeFry2x64Test.Logical
32: [ OK ] ThreeFry2x64Test.Logical (0 ms)
32: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
32: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms)
32: [ RUN ] ThreeFry2x64Test.Reseed
32: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
32: [ RUN ] ThreeFry2x64Test.Discard
32: [ OK ] ThreeFry2x64Test.Discard (1 ms)
32: [ RUN ] ThreeFry2x64Test.InvalidCounter
32: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
32: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
32: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
32: [----------] 6 tests from ThreeFry2x64Test (1 ms total)
32:
32: [----------] 4 tests from UniformIntDistributionTest
32: [ RUN ] UniformIntDistributionTest.Output
32: [ OK ] UniformIntDistributionTest.Output (0 ms)
32: [ RUN ] UniformIntDistributionTest.Logical
32: [ OK ] UniformIntDistributionTest.Logical (0 ms)
32: [ RUN ] UniformIntDistributionTest.Reset
32: [ OK ] UniformIntDistributionTest.Reset (0 ms)
32: [ RUN ] UniformIntDistributionTest.AltParam
32: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from UniformIntDistributionTest (0 ms total)
32:
32: [----------] 5 tests from UniformRealDistributionTest
32: [ RUN ] UniformRealDistributionTest.GenerateCanonical
32: [ OK ] UniformRealDistributionTest.GenerateCanonical (1 ms)
32: [ RUN ] UniformRealDistributionTest.Output
32: [ OK ] UniformRealDistributionTest.Output (0 ms)
32: [ RUN ] UniformRealDistributionTest.Logical
32: [ OK ] UniformRealDistributionTest.Logical (0 ms)
32: [ RUN ] UniformRealDistributionTest.Reset
32: [ OK ] UniformRealDistributionTest.Reset (0 ms)
32: [ RUN ] UniformRealDistributionTest.AltParam
32: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
32: [----------] 5 tests from UniformRealDistributionTest (1 ms total)
32:
32: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
32: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (2 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 44 tests from 10 test cases ran. (10 ms total)
32: [ PASSED ] 44 tests.
32/65 Test #32: RandomUnitTests ....................... Passed 0.06 sec
test 33
Start 33: RestraintTests
33: Test command: /<<PKGBUILDDIR>>/build/basic/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RestraintTests.xml"
33: Test timeout computed to be: 30
33: [==========] Running 1 test from 1 test case.
33: [----------] Global test environment set-up.
33: [----------] 1 test from RestraintManager
33: [ RUN ] RestraintManager.restraintList
33: [ OK ] RestraintManager.restraintList (0 ms)
33: [----------] 1 test from RestraintManager (0 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 1 test from 1 test case ran. (0 ms total)
33: [ PASSED ] 1 test.
33/65 Test #33: RestraintTests ........................ Passed 0.03 sec
test 34
Start 34: TableUnitTests
34: Test command: /<<PKGBUILDDIR>>/build/basic/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TableUnitTests.xml"
34: Test timeout computed to be: 30
34: [==========] Running 16 tests from 2 test cases.
34: [----------] Global test environment set-up.
34: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
34: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
34: [ OK ] SplineTableTest/0.HandlesIncorrectInput (3 ms)
34: [ RUN ] SplineTableTest/0.Sinc
34: [ OK ] SplineTableTest/0.Sinc (1 ms)
34: [ RUN ] SplineTableTest/0.LJ12
34: [ OK ] SplineTableTest/0.LJ12 (36 ms)
34: [ RUN ] SplineTableTest/0.PmeCorrection
34: [ OK ] SplineTableTest/0.PmeCorrection (3 ms)
34: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
34: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms)
34: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
34: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (3 ms)
34: [ RUN ] SplineTableTest/0.TwoFunctions
34: [ OK ] SplineTableTest/0.TwoFunctions (89 ms)
34: [ RUN ] SplineTableTest/0.ThreeFunctions
34: [ OK ] SplineTableTest/0.ThreeFunctions (83 ms)
34: [----------] 8 tests from SplineTableTest/0 (219 ms total)
34:
34: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
34: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
34: [ OK ] SplineTableTest/1.HandlesIncorrectInput (2 ms)
34: [ RUN ] SplineTableTest/1.Sinc
34: [ OK ] SplineTableTest/1.Sinc (2 ms)
34: [ RUN ] SplineTableTest/1.LJ12
34: [ OK ] SplineTableTest/1.LJ12 (4 ms)
34: [ RUN ] SplineTableTest/1.PmeCorrection
34: [ OK ] SplineTableTest/1.PmeCorrection (3 ms)
34: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
34: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms)
34: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
34: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms)
34: [ RUN ] SplineTableTest/1.TwoFunctions
34: [ OK ] SplineTableTest/1.TwoFunctions (10 ms)
34: [ RUN ] SplineTableTest/1.ThreeFunctions
34: [ OK ] SplineTableTest/1.ThreeFunctions (14 ms)
34: [----------] 8 tests from SplineTableTest/1 (38 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 16 tests from 2 test cases ran. (257 ms total)
34: [ PASSED ] 16 tests.
34/65 Test #34: TableUnitTests ........................ Passed 0.29 sec
test 35
Start 35: TaskAssignmentUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 3 tests from 2 test cases.
35: [----------] Global test environment set-up.
35: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
35: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
35: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (1 ms)
35: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
35: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
35: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (1 ms total)
35:
35: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
35: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
35: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (1 ms)
35: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (1 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 3 tests from 2 test cases ran. (2 ms total)
35: [ PASSED ] 3 tests.
35/65 Test #35: TaskAssignmentUnitTests ............... Passed 0.04 sec
test 36
Start 36: TopologyTest
36: Test command: /<<PKGBUILDDIR>>/build/basic/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TopologyTest.xml"
36: Test timeout computed to be: 30
36: [==========] Running 31 tests from 5 test cases.
36: [----------] Global test environment set-up.
36: [----------] 3 tests from ExclusionBlockTest
36: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
36: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
36: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
36: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
36: [ RUN ] ExclusionBlockTest.MergeExclusions
36: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
36: [----------] 3 tests from ExclusionBlockTest (0 ms total)
36:
36: [----------] 6 tests from InteractionListTest
36: [ RUN ] InteractionListTest.EmptyWorks
36: [ OK ] InteractionListTest.EmptyWorks (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionArray
36: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms
36: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionPointer
36: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms)
36: [ RUN ] InteractionListTest.CanAddListToOtherList
36: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms)
36: [ RUN ] InteractionListTest.ClearingWorks
36: [ OK ] InteractionListTest.ClearingWorks (0 ms)
36: [----------] 6 tests from InteractionListTest (1 ms total)
36:
36: [----------] 3 tests from MtopTest
36: [ RUN ] MtopTest.RangeBasedLoop
36: [ OK ] MtopTest.RangeBasedLoop (0 ms)
36: [ RUN ] MtopTest.Operators
36: [ OK ] MtopTest.Operators (0 ms)
36: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms
36: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms)
36: [----------] 3 tests from MtopTest (0 ms total)
36:
36: [----------] 13 tests from StringTableTest
36: [ RUN ] StringTableTest.AddSingleEntry
36: [ OK ] StringTableTest.AddSingleEntry (1 ms)
36: [ RUN ] StringTableTest.CanAccessWithAt
36: [ OK ] StringTableTest.CanAccessWithAt (1 ms)
36: [ RUN ] StringTableTest.CanAccessWithBracket
36: [ OK ] StringTableTest.CanAccessWithBracket (0 ms)
36: [ RUN ] StringTableTest.ThrowsOutOfRange
36: [ OK ] StringTableTest.ThrowsOutOfRange (1 ms)
36: [ RUN ] StringTableTest.StringCompareIsCorrect
36: [ OK ] StringTableTest.StringCompareIsCorrect (1 ms)
36: [ RUN ] StringTableTest.AddTwoDistinctEntries
36: [ OK ] StringTableTest.AddTwoDistinctEntries (1 ms)
36: [ RUN ] StringTableTest.TryToAddDuplicates
36: [ OK ] StringTableTest.TryToAddDuplicates (0 ms)
36: [ RUN ] StringTableTest.AddLargeNumberOfEntries
36: [ OK ] StringTableTest.AddLargeNumberOfEntries (1 ms)
36: [ RUN ] StringTableTest.NoDuplicatesInLargeTable
36: [ OK ] StringTableTest.NoDuplicatesInLargeTable (1 ms)
36: [ RUN ] StringTableTest.CanWriteToBuffer
36: [ OK ] StringTableTest.CanWriteToBuffer (0 ms)
36: [ RUN ] StringTableTest.Roundtrip
36: [ OK ] StringTableTest.Roundtrip (0 ms)
36: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices
36: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms)
36: [ RUN ] StringTableTest.CanCopyToLegacyTable
36: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms)
36: [----------] 13 tests from StringTableTest (7 ms total)
36:
36: [----------] 6 tests from LegacySymtabTest
36: [ RUN ] LegacySymtabTest.EmptyOnOpen
36: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms)
36: [ RUN ] LegacySymtabTest.AddSingleEntry
36: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms)
36: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries
36: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms)
36: [ RUN ] LegacySymtabTest.TryToAddDuplicates
36: [ OK ] LegacySymtabTest.TryToAddDuplicates (1 ms)
36: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries
36: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms)
36: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable
36: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms)
36: [----------] 6 tests from LegacySymtabTest (1 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 31 tests from 5 test cases ran. (9 ms total)
36: [ PASSED ] 31 tests.
36/65 Test #36: TopologyTest .......................... Passed 0.05 sec
test 37
Start 37: PullTest
37: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PullTest.xml"
37: Test timeout computed to be: 30
37: [==========] Running 5 tests from 1 test case.
37: [----------] Global test environment set-up.
37: [----------] 5 tests from PullTest
37: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
37: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (1 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
37: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
37: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
37: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
37: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
37: [----------] 5 tests from PullTest (1 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 5 tests from 1 test case ran. (1 ms total)
37: [ PASSED ] 5 tests.
37/65 Test #37: PullTest .............................. Passed 0.03 sec
test 38
Start 38: SimdUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SimdUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 86 tests from 3 test cases.
38: [----------] Global test environment set-up.
38: [----------] 41 tests from SimdScalarTest
38: [ RUN ] SimdScalarTest.load
38: [ OK ] SimdScalarTest.load (0 ms)
38: [ RUN ] SimdScalarTest.loadU
38: [ OK ] SimdScalarTest.loadU (0 ms)
38: [ RUN ] SimdScalarTest.store
38: [ OK ] SimdScalarTest.store (0 ms)
38: [ RUN ] SimdScalarTest.storeU
38: [ OK ] SimdScalarTest.storeU (0 ms)
38: [ RUN ] SimdScalarTest.setZero
38: [ OK ] SimdScalarTest.setZero (0 ms)
38: [ RUN ] SimdScalarTest.andNot
38: [ OK ] SimdScalarTest.andNot (0 ms)
38: [ RUN ] SimdScalarTest.fma
38: [ OK ] SimdScalarTest.fma (0 ms)
38: [ RUN ] SimdScalarTest.fms
38: [ OK ] SimdScalarTest.fms (0 ms)
38: [ RUN ] SimdScalarTest.fnma
38: [ OK ] SimdScalarTest.fnma (0 ms)
38: [ RUN ] SimdScalarTest.fnms
38: [ OK ] SimdScalarTest.fnms (0 ms)
38: [ RUN ] SimdScalarTest.maskAdd
38: [ OK ] SimdScalarTest.maskAdd (0 ms)
38: [ RUN ] SimdScalarTest.maskzMul
38: [ OK ] SimdScalarTest.maskzMul (0 ms)
38: [ RUN ] SimdScalarTest.maskzFma
38: [ OK ] SimdScalarTest.maskzFma (0 ms)
38: [ RUN ] SimdScalarTest.abs
38: [ OK ] SimdScalarTest.abs (0 ms)
38: [ RUN ] SimdScalarTest.max
38: [ OK ] SimdScalarTest.max (0 ms)
38: [ RUN ] SimdScalarTest.min
38: [ OK ] SimdScalarTest.min (0 ms)
38: [ RUN ] SimdScalarTest.round
38: [ OK ] SimdScalarTest.round (0 ms)
38: [ RUN ] SimdScalarTest.trunc
38: [ OK ] SimdScalarTest.trunc (0 ms)
38: [ RUN ] SimdScalarTest.reduce
38: [ OK ] SimdScalarTest.reduce (0 ms)
38: [ RUN ] SimdScalarTest.testBits
38: [ OK ] SimdScalarTest.testBits (0 ms)
38: [ RUN ] SimdScalarTest.anyTrue
38: [ OK ] SimdScalarTest.anyTrue (0 ms)
38: [ RUN ] SimdScalarTest.selectByMask
38: [ OK ] SimdScalarTest.selectByMask (0 ms)
38: [ RUN ] SimdScalarTest.selectByNotMask
38: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
38: [ RUN ] SimdScalarTest.blend
38: [ OK ] SimdScalarTest.blend (0 ms)
38: [ RUN ] SimdScalarTest.cvtR2I
38: [ OK ] SimdScalarTest.cvtR2I (0 ms)
38: [ RUN ] SimdScalarTest.cvttR2I
38: [ OK ] SimdScalarTest.cvttR2I (0 ms)
38: [ RUN ] SimdScalarTest.cvtI2R
38: [ OK ] SimdScalarTest.cvtI2R (0 ms)
38: [ RUN ] SimdScalarTest.cvtF2D
38: [ OK ] SimdScalarTest.cvtF2D (0 ms)
38: [ RUN ] SimdScalarTest.cvtD2D
38: [ OK ] SimdScalarTest.cvtD2D (0 ms)
38: [ RUN ] SimdScalarTest.loadI
38: [ OK ] SimdScalarTest.loadI (0 ms)
38: [ RUN ] SimdScalarTest.loadUI
38: [ OK ] SimdScalarTest.loadUI (0 ms)
38: [ RUN ] SimdScalarTest.storeI
38: [ OK ] SimdScalarTest.storeI (0 ms)
38: [ RUN ] SimdScalarTest.storeUI
38: [ OK ] SimdScalarTest.storeUI (0 ms)
38: [ RUN ] SimdScalarTest.andNotI
38: [ OK ] SimdScalarTest.andNotI (0 ms)
38: [ RUN ] SimdScalarTest.testBitsI
38: [ OK ] SimdScalarTest.testBitsI (0 ms)
38: [ RUN ] SimdScalarTest.selectByMaskI
38: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
38: [ RUN ] SimdScalarTest.selectByNotMaskI
38: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
38: [ RUN ] SimdScalarTest.blendI
38: [ OK ] SimdScalarTest.blendI (0 ms)
38: [ RUN ] SimdScalarTest.cvtB2IB
38: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
38: [ RUN ] SimdScalarTest.cvtIB2B
38: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
38: [ RUN ] SimdScalarTest.expandScalarsToTriplets
38: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
38: [----------] 41 tests from SimdScalarTest (1 ms total)
38:
38: [----------] 8 tests from SimdScalarUtilTest
38: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
38: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
38: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
38: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
38: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
38: [----------] 8 tests from SimdScalarUtilTest (0 ms total)
38:
38: [----------] 37 tests from SimdScalarMathTest
38: [ RUN ] SimdScalarMathTest.copysign
38: [ OK ] SimdScalarMathTest.copysign (0 ms)
38: [ RUN ] SimdScalarMathTest.invsqrtPair
38: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
38: [ RUN ] SimdScalarMathTest.inv
38: [ OK ] SimdScalarMathTest.inv (0 ms)
38: [ RUN ] SimdScalarMathTest.maskzInvsqrt
38: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
38: [ RUN ] SimdScalarMathTest.log
38: [ OK ] SimdScalarMathTest.log (0 ms)
38: [ RUN ] SimdScalarMathTest.exp2
38: [ OK ] SimdScalarMathTest.exp2 (0 ms)
38: [ RUN ] SimdScalarMathTest.exp
38: [ OK ] SimdScalarMathTest.exp (0 ms)
38: [ RUN ] SimdScalarMathTest.erf
38: [ OK ] SimdScalarMathTest.erf (0 ms)
38: [ RUN ] SimdScalarMathTest.erfc
38: [ OK ] SimdScalarMathTest.erfc (0 ms)
38: [ RUN ] SimdScalarMathTest.sincos
38: [ OK ] SimdScalarMathTest.sincos (0 ms)
38: [ RUN ] SimdScalarMathTest.sin
38: [ OK ] SimdScalarMathTest.sin (0 ms)
38: [ RUN ] SimdScalarMathTest.cos
38: [ OK ] SimdScalarMathTest.cos (0 ms)
38: [ RUN ] SimdScalarMathTest.tan
38: [ OK ] SimdScalarMathTest.tan (0 ms)
38: [ RUN ] SimdScalarMathTest.asin
38: [ OK ] SimdScalarMathTest.asin (0 ms)
38: [ RUN ] SimdScalarMathTest.acos
38: [ OK ] SimdScalarMathTest.acos (0 ms)
38: [ RUN ] SimdScalarMathTest.atan
38: [ OK ] SimdScalarMathTest.atan (0 ms)
38: [ RUN ] SimdScalarMathTest.atan2
38: [ OK ] SimdScalarMathTest.atan2 (0 ms)
38: [ RUN ] SimdScalarMathTest.pmeForceCorrection
38: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
38: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
38: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
38: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
38: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.invSingleAccuracy
38: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
38: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.logSingleAccuracy
38: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
38: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.expSingleAccuracy
38: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
38: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
38: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
38: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
38: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
38: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
38: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
38: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
38: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
38: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
38: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
38: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
38: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
38: [----------] 37 tests from SimdScalarMathTest (1 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 86 tests from 3 test cases ran. (3 ms total)
38: [ PASSED ] 86 tests.
38/65 Test #38: SimdUnitTests ......................... Passed 0.04 sec
test 39
Start 39: CompatibilityHelpersTests
39: Test command: /<<PKGBUILDDIR>>/build/basic/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 9 tests from 6 test cases.
39: [----------] Global test environment set-up.
39: [----------] 4 tests from TemplateMPTest
39: [ RUN ] TemplateMPTest.MpWithIndexInt
39: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexIntBad
39: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexBool
39: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexEnum
39: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms)
39: [----------] 4 tests from TemplateMPTest (0 ms total)
39:
39: [----------] 1 test from NotNullConstruction
39: [ RUN ] NotNullConstruction.Works
39: [ OK ] NotNullConstruction.Works (0 ms)
39: [----------] 1 test from NotNullConstruction (0 ms total)
39:
39: [----------] 1 test from NotNullCasting
39: [ RUN ] NotNullCasting.Works
39: [ OK ] NotNullCasting.Works (0 ms)
39: [----------] 1 test from NotNullCasting (0 ms total)
39:
39: [----------] 1 test from NotNullAssignment
39: [ RUN ] NotNullAssignment.Works
39: [ OK ] NotNullAssignment.Works (0 ms)
39: [----------] 1 test from NotNullAssignment (0 ms total)
39:
39: [----------] 1 test from MakeNotNull
39: [ RUN ] MakeNotNull.Works
39: [ OK ] MakeNotNull.Works (0 ms)
39: [----------] 1 test from MakeNotNull (0 ms total)
39:
39: [----------] 1 test from NotNull
39: [ RUN ] NotNull.WorksInContainers
39: [ OK ] NotNull.WorksInContainers (0 ms)
39: [----------] 1 test from NotNull (0 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 9 tests from 6 test cases ran. (0 ms total)
39: [ PASSED ] 9 tests.
39/65 Test #39: CompatibilityHelpersTests ............. Passed 0.03 sec
test 40
Start 40: GmxAnaTest
40: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxAnaTest.xml"
40: Test timeout computed to be: 600
40: [==========] Running 27 tests from 5 test cases.
40: [----------] Global test environment set-up.
40: [----------] 5 tests from Entropy
40: [ RUN ] Entropy.Schlitter_300_NoLinear
40: [ OK ] Entropy.Schlitter_300_NoLinear (4 ms)
40: [ RUN ] Entropy.Schlitter_300_Linear
40: [ OK ] Entropy.Schlitter_300_Linear (0 ms)
40: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
40: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (1 ms)
40: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
40: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms)
40: [ RUN ] Entropy.QuasiHarmonic_200_Linear
40: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms)
40: [----------] 5 tests from Entropy (5 ms total)
40:
40: [----------] 10 tests from MindistTest
40: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistWorksWithSingleAtoms (77 ms)
40: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 2: 'atom3'
40: Selected 3: 'atoms12'
40: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (3 ms)
40: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistDoesNotPickUpContacts (4 ms)
40: [ RUN ] MindistTest.mindistPicksUpContacts
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistPicksUpContacts (4 ms)
40: [ RUN ] MindistTest.ngWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.ngWorks (3 ms)
40: [ RUN ] MindistTest.groupWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 3: 'atoms12'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.groupWorks (4 ms)
40: [ RUN ] MindistTest.maxDistWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 2: 'atom3'
40: Selected 3: 'atoms12'
40: [ OK ] MindistTest.maxDistWorks (3 ms)
40: [ RUN ] MindistTest.noPbcWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.noPbcWorks (3 ms)
40: [ RUN ] MindistTest.resPerTimeWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 3: 'atoms12'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.resPerTimeWorks (4 ms)
40: [ RUN ] MindistTest.matrixWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 5: 'atoms123'
40: Special case: making distance matrix between all atoms in group atoms123
40: [ OK ] MindistTest.matrixWorks (3 ms)
40: [----------] 10 tests from MindistTest (108 ms total)
40:
40: [----------] 3 tests from MsdTest
40: [ RUN ] MsdTest.threeDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.threeDimensionalDiffusion (4 ms)
40: [ RUN ] MsdTest.twoDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.twoDimensionalDiffusion (3 ms)
40: [ RUN ] MsdTest.oneDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.oneDimensionalDiffusion (3 ms)
40: [----------] 3 tests from MsdTest (10 ms total)
40:
40: [----------] 3 tests from MsdMolTest
40: [ RUN ] MsdMolTest.diffMolMassWeighted
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( water) has 15 elements
40: There is one group in the index
40: Split group of 15 atoms into 5 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to 1543356362
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted_msdmol.xvg
40: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolMassWeighted (1956 ms)
40: [ RUN ] MsdMolTest.diffMolNonMassWeighted
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( water) has 15 elements
40: There is one group in the index
40: Split group of 15 atoms into 5 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -748763461
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted_msdmol.xvg
40: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolNonMassWeighted (1841 ms)
40: [ RUN ] MsdMolTest.diffMolSelected
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( mol) has 9 elements
40: There is one group in the index
40: Split group of 9 atoms into 3 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -302681669
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected_msdmol.xvg
40: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ mol] 7.8614 (+/- 1.5618) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolSelected (1744 ms)
40: [----------] 3 tests from MsdMolTest (5545 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: trr version: GMX_trn_file (single precision)
40:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (31 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (6 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (5 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (5 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (5 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (5 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (57 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 27 tests from 5 test cases ran. (5726 ms total)
40: [ PASSED ] 27 tests.
40/65 Test #40: GmxAnaTest ............................ Passed 5.76 sec
test 41
Start 41: GmxPreprocessTests
41: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxPreprocessTests.xml"
41: Test timeout computed to be: 1920
41: [==========] Running 69 tests from 10 test cases.
41: [----------] Global test environment set-up.
41: [----------] 4 tests from GenconfTest
41: [ RUN ] GenconfTest.nbox_Works
41: [ OK ] GenconfTest.nbox_Works (11 ms)
41: [ RUN ] GenconfTest.nbox_norenumber_Works
41: [ OK ] GenconfTest.nbox_norenumber_Works (3 ms)
41: [ RUN ] GenconfTest.nbox_dist_Works
41: [ OK ] GenconfTest.nbox_dist_Works (14 ms)
41: [ RUN ] GenconfTest.nbox_rot_Works
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: [ OK ] GenconfTest.nbox_rot_Works (7 ms)
41: [----------] 4 tests from GenconfTest (38 ms total)
41:
41: [----------] 2 tests from GenionTest
41: [ RUN ] GenionTest.HighConcentrationIonPlacement
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
41: buffer. The cluster pair list does have a buffering effect, but choosing
41: a larger rlist might be necessary for good energy conservation.
41:
41:
41: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: Generating 1-4 interactions: fudge = 0.5
41: Number of degrees of freedom in T-Coupling group rest is 1308.00
41:
41: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: You are using a plain Coulomb cut-off, which might produce artifacts.
41: You might want to consider using PME electrostatics.
41:
41:
41:
41: There were 3 notes
41: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
41: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
41: Group 0 ( System) has 653 elements
41: Group 1 ( Water) has 648 elements
41: Group 2 ( SOL) has 648 elements
41: Group 3 ( non-Water) has 5 elements
41: Group 4 ( Other) has 5 elements
41: Group 5 ( METH) has 5 elements
41: Select a group: Number of (3-atomic) solvent molecules: 216
41: Using random seed 1997.
41: Replacing solvent molecule 56 (atom 168) with NA
41: Replacing solvent molecule 120 (atom 360) with NA
41: Replacing solvent molecule 182 (atom 546) with NA
41: Replacing solvent molecule 71 (atom 213) with NA
41: Replacing solvent molecule 189 (atom 567) with CL
41: Replacing solvent molecule 54 (atom 162) with CL
41: Replacing solvent molecule 155 (atom 465) with CL
41: Replacing solvent molecule 99 (atom 297) with CL
41:
41: Setting the LD random seed to -638610193
41:
41: Generated 331705 of the 331705 non-bonded parameter combinations
41:
41: Generated 331705 of the 331705 1-4 parameter combinations
41:
41: Excluding 2 bonded neighbours molecule type 'SOL'
41:
41: Excluding 3 bonded neighbours molecule type 'methane'
41: Analysing residue names:
41: There are: 216 Water residues
41: There are: 1 Other residues
41: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
41:
41: This run will generate roughly 0 Mb of data
41: Will try to add 4 NA ions and 4 CL ions.
41: Select a continuous group of solvent molecules
41: Selected 1: 'Water'
41: [ OK ] GenionTest.HighConcentrationIonPlacement (1930 ms)
41: [ RUN ] GenionTest.NoIonPlacement
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
41: buffer. The cluster pair list does have a buffering effect, but choosing
41: a larger rlist might be necessary for good energy conservation.
41:
41:
41: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: Generating 1-4 interactions: fudge = 0.5
41: Number of degrees of freedom in T-Coupling group rest is 1308.00
41:
41: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: You are using a plain Coulomb cut-off, which might produce artifacts.
41: You might want to consider using PME electrostatics.
41:
41:
41:
41: There were 3 notes
41: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
41: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
41: No ions to add, will just copy input configuration.
41: Setting the LD random seed to -545786603
41:
41: Generated 331705 of the 331705 non-bonded parameter combinations
41:
41: Generated 331705 of the 331705 1-4 parameter combinations
41:
41: Excluding 2 bonded neighbours molecule type 'SOL'
41:
41: Excluding 3 bonded neighbours molecule type 'methane'
41: Analysing residue names:
41: There are: 216 Water residues
41: There are: 1 Other residues
41: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
41:
41: This run will generate roughly 0 Mb of data
41: [ OK ] GenionTest.NoIonPlacement (1911 ms)
41: [----------] 2 tests from GenionTest (3842 ms total)
41:
41: [----------] 1 test from GenRestrTest
41: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
41:
41: Reading structure file
41: Group 0 ( System) has 156 elements
41: Group 1 ( Protein) has 156 elements
41: Group 2 ( Protein-H) has 75 elements
41: Group 3 ( C-alpha) has 10 elements
41: Group 4 ( Backbone) has 30 elements
41: Group 5 ( MainChain) has 40 elements
41: Group 6 ( MainChain+Cb) has 49 elements
41: Group 7 ( MainChain+H) has 52 elements
41: Group 8 ( SideChain) has 104 elements
41: Group 9 ( SideChain-H) has 35 elements
41: Select a group: Select group to position restrain
41: Selected 3: 'C-alpha'
41: [ OK ] GenRestrTest.SimpleRestraintsGenerated (12 ms)
41: [----------] 1 test from GenRestrTest (12 ms total)
41:
41: [----------] 9 tests from PreprocessingAtomTypesTest
41: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
41: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
41: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
41: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
41: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
41: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
41: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
41: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
41: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
41: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
41: [----------] 9 tests from PreprocessingAtomTypesTest (2 ms total)
41:
41: [----------] 10 tests from PreprocessingBondAtomTypeTest
41: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
41: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
41: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
41: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
41: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
41: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
41: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
41: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
41: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
41: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
41: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
41: [----------] 10 tests from PreprocessingBondAtomTypeTest (2 ms total)
41:
41: [----------] 5 tests from InsertMoleculesTest
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 8 atoms)!
41:
41: Added 1 molecules (out of 1 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
41:
41: Output configuration contains 8 atoms in 4 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (6 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 2 atoms)!
41:
Try 2 success (now 4 atoms)!
41:
Try 3 success (now 6 atoms)!
41:
Try 4 success (now 8 atoms)!
41:
Try 5 success (now 10 atoms)!
41:
41: Added 5 molecules (out of 5 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
41:
41: Output configuration contains 10 atoms in 10 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (5 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 8 atoms)!
41:
Try 2 success (now 10 atoms)!
41:
41: Added 2 molecules (out of 2 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
41:
41: Output configuration contains 10 atoms in 4 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (6 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 650 atoms)!
41:
Try 2 success (now 652 atoms)!
41:
Try 3 success (now 654 atoms)!
41:
Try 4 success (now 656 atoms)!
41:
41: Added 4 molecules (out of 4 requested)
41: Replaced 8 residues (24 atoms)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
41:
41: Output configuration contains 632 atoms in 212 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (107 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
41:
41:
Try 1 success (now 2 atoms)!
41:
Try 2 success (now 4 atoms)!
41:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
41:
Try 13 success (now 6 atoms)!
41:
41: Added 3 molecules (out of 4 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
41:
41: Output configuration contains 6 atoms in 3 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (6 ms)
41: [----------] 5 tests from InsertMoleculesTest (131 ms total)
41:
41: [----------] 14 tests from GetIrTest
41: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
41: Ignoring obsolete mdp entry 'title'
41: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (12 ms)
41: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
41: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (15 ms)
41: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsKeyWithoutValue (14 ms)
41: [ RUN ] GetIrTest.RejectsValueWithoutKey
41: [ OK ] GetIrTest.RejectsValueWithoutKey (14 ms)
41: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
41: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (14 ms)
41: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (9 ms)
41: [ RUN ] GetIrTest.AcceptsEmptyLines
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsEmptyLines (8 ms)
41: [ RUN ] GetIrTest.AcceptsElectricField
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricField (16 ms)
41: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (12 ms)
41: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (8 ms)
41: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
41: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (7 ms)
41: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsImplicitSolventNo (8 ms)
41: [ RUN ] GetIrTest.RejectsImplicitSolventYes
41: [ OK ] GetIrTest.RejectsImplicitSolventYes (15 ms)
41: [ RUN ] GetIrTest.AcceptsMimic
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsMimic (10 ms)
41: [----------] 14 tests from GetIrTest (165 ms total)
41:
41: [----------] 5 tests from SolvateTest
41: [ RUN ] SolvateTest.cs_box_Works
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 1x1x1 boxes
41: Solvent box contains 270 atoms in 90 residues
41: Removed 129 solvent atoms due to solvent-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 47 residues
41: Generated solvent containing 141 atoms in 47 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
41:
41: Output configuration contains 141 atoms in 47 residues
41: Volume : 1.331 (nm^3)
41: Density : 1056.36 (g/l)
41: Number of solvent molecules: 47
41:
41: [ OK ] SolvateTest.cs_box_Works (48 ms)
41: [ RUN ] SolvateTest.cs_cp_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 886 residues
41: Generated solvent containing 2658 atoms in 886 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
41:
41: Output configuration contains 2664 atoms in 888 residues
41: Volume : 27.2709 (nm^3)
41: Density : 974.777 (g/l)
41: Number of solvent molecules: 886
41:
41: [ OK ] SolvateTest.cs_cp_Works (174 ms)
41: [ RUN ] SolvateTest.cs_cp_p_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 886 residues
41: Generated solvent containing 2658 atoms in 886 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
41:
41: Output configuration contains 2664 atoms in 888 residues
41: Volume : 27.2709 (nm^3)
41: Density : 974.777 (g/l)
41: Number of solvent molecules: 886
41:
41: Processing topology
41: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
41: [ OK ] SolvateTest.cs_cp_p_Works (175 ms)
41: [ RUN ] SolvateTest.shell_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 1902 solvent atoms more than 1.000000 nm from solute.
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 252 residues
41: Generated solvent containing 756 atoms in 252 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
41:
41: Output configuration contains 762 atoms in 254 residues
41: Volume : 27.2709 (nm^3)
41: Density : 279.3 (g/l)
41: Number of solvent molecules: 252
41:
41: [ OK ] SolvateTest.shell_Works (63 ms)
41: [ RUN ] SolvateTest.update_Topology_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 3x3x3 boxes
41: Solvent box contains 14952 atoms in 4984 residues
41: Removed 2787 solvent atoms due to solvent-solvent overlap
41: Removed 30 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 2 different molecule types:
41: HOH ( 3 atoms): 1876 residues
41: SOL ( 3 atoms): 2169 residues
41: Generated solvent containing 0 atoms in 0 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
41:
41: Output configuration contains 12141 atoms in 4047 residues
41: Volume : 125 (nm^3)
41: Density : 968.963 (g/l)
41: Number of solvent molecules: 4045
41:
41: Processing topology
41: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
41: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
41: [ OK ] SolvateTest.update_Topology_Works (672 ms)
41: [----------] 5 tests from SolvateTest (1132 ms total)
41:
41: [----------] 1 test from TopDirTests
41: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
41: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
41: [----------] 1 test from TopDirTests (0 ms total)
41:
41: [----------] 18 tests from SinglePeptideFragments/EditconfTest
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (184 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (21 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (21 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (17 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (8 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (8 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (11 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (14 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (20 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (16 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (15 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (14 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (8 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (6 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (5 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (9 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (6 ms)
41: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8
41:
41: Select a group for output:
41: Group 0 ( two_residues) has 23 elements
41: There is one group in the index
41: Note that major changes are planned in future for editconf, to improve usability and utility.
41: Read 252 atoms
41: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
41: No velocities found
41: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (7 ms)
41: [----------] 18 tests from SinglePeptideFragments/EditconfTest (391 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 69 tests from 10 test cases ran. (5718 ms total)
41: [ PASSED ] 69 tests.
41/65 Test #41: GmxPreprocessTests .................... Passed 5.76 sec
test 42
Start 42: Pdb2gmx1Test
42: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx1Test.xml"
42: Test timeout computed to be: 1920
42: [==========] Running 24 tests from 1 test case.
42: [----------] Global test environment set-up.
42: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (323 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (314 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (270 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (247 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (305 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (336 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (270 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (256 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (293 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (322 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (300 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (313 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (311 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (375 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (327 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (324 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (266 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (295 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (347 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (257 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (271 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (297 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (290 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge -0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (265 ms)
42: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (7177 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 24 tests from 1 test case ran. (7177 ms total)
42: [ PASSED ] 24 tests.
42/65 Test #42: Pdb2gmx1Test .......................... Passed 7.21 sec
test 43
Start 43: Pdb2gmx2Test
43: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx2Test.xml"
43: Test timeout computed to be: 1920
43: [==========] Running 32 tests from 2 test cases.
43: [----------] Global test environment set-up.
43: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (179 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (222 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (187 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (187 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 37 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 37 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (245 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 53 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 51 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (257 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 36 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 36 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (214 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 33 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 31 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (196 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (164 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (194 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (156 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (138 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 37 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 37 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (173 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 53 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 51 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (192 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 36 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 36 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (179 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 33 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 31 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (224 ms)
43: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (3113 ms total)
43:
43: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (203 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (264 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (211 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (175 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 39 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 39 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (170 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 57 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 55 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (215 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 38 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 38 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (223 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 35 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 33 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (162 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (204 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (185 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (170 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (179 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 39 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 39 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (172 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 57 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 55 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (219 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 38 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 38 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (215 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 35 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 33 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (211 ms)
43: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (3178 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 32 tests from 2 test cases ran. (6291 ms total)
43: [ PASSED ] 32 tests.
43/65 Test #43: Pdb2gmx2Test .......................... Passed 6.33 sec
test 44
Start 44: Pdb2gmx3Test
44: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx3Test.xml"
44: Test timeout computed to be: 1920
44: [==========] Running 33 tests from 6 test cases.
44: [----------] Global test environment set-up.
44: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 653 pairs
44: Before cleaning: 691 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 255, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 691 dihedrals, 51 impropers, 457 angles
44: 650 pairs, 254 bonds and 0 virtual sites
44:
44: Total mass 1846.132 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (422 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 748 pairs
44: Before cleaning: 788 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 291, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 788 dihedrals, 72 impropers, 516 angles
44: 736 pairs, 290 bonds and 0 virtual sites
44:
44: Total mass 2088.366 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (290 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 676 pairs
44: Before cleaning: 727 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 262, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 727 dihedrals, 56 impropers, 472 angles
44: 667 pairs, 261 bonds and 0 virtual sites
44:
44: Total mass 1861.124 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (245 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 603 pairs
44: Before cleaning: 634 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 233, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 634 dihedrals, 48 impropers, 419 angles
44: 597 pairs, 232 bonds and 0 virtual sites
44:
44: Total mass 1662.888 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (212 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 124 virtual sites
44: Added 16 dummy masses
44: Added 26 new constraints
44: Before cleaning: 653 pairs
44: Before cleaning: 691 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 255, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 691 dihedrals, 51 impropers, 457 angles
44: 650 pairs, 254 bonds and 130 virtual sites
44:
44: Total mass 1846.132 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (249 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 132 virtual sites
44: Added 10 dummy masses
44: Added 19 new constraints
44: Before cleaning: 748 pairs
44: Before cleaning: 788 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 291, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 788 dihedrals, 72 impropers, 516 angles
44: 736 pairs, 290 bonds and 133 virtual sites
44:
44: Total mass 2088.366 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (264 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 123 virtual sites
44: Added 22 dummy masses
44: Added 35 new constraints
44: Before cleaning: 676 pairs
44: Before cleaning: 727 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 262, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 727 dihedrals, 56 impropers, 472 angles
44: 667 pairs, 261 bonds and 132 virtual sites
44:
44: Total mass 1861.124 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (242 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 111 virtual sites
44: Added 18 dummy masses
44: Added 31 new constraints
44: Before cleaning: 603 pairs
44: Before cleaning: 634 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 233, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 634 dihedrals, 48 impropers, 419 angles
44: 597 pairs, 232 bonds and 116 virtual sites
44:
44: Total mass 1662.888 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (256 ms)
44: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (2186 ms total)
44:
44: [----------] 1 test from ForAmber99sb_ildnWithTip4p/Pdb2gmxTest
44: [ RUN ] ForAmber99sb_ildnWithTip4p/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/tip4p.pdb...
44: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 2 4 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (4 atoms, 2 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 2 residues with 8 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 4, now 4
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 2 angles
44: 0 pairs, 4 bonds and 0 virtual sites
44:
44: Total mass 36.032 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/tip4p.pdb.
44:
44: The Amber99sb-ildn force field and the tip4p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildnWithTip4p/Pdb2gmxTest.ProducesMatchingTopology/0 (71 ms)
44: [----------] 1 test from ForAmber99sb_ildnWithTip4p/Pdb2gmxTest (72 ms total)
44:
44: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 653 pairs
44: Before cleaning: 663 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 254, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 663 dihedrals, 48 impropers, 457 angles
44: 650 pairs, 254 bonds and 0 virtual sites
44:
44: Total mass 1846.115 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (214 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 748 pairs
44: Before cleaning: 778 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus PHE-33: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 290, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 778 dihedrals, 49 impropers, 516 angles
44: 736 pairs, 290 bonds and 0 virtual sites
44:
44: Total mass 2088.361 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (245 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 676 pairs
44: Before cleaning: 696 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44: Start terminus ALA-34: NH3+
44: End terminus ALA-49: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 261, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 696 dihedrals, 39 impropers, 472 angles
44: 667 pairs, 261 bonds and 0 virtual sites
44:
44: Total mass 1861.130 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (244 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 603 pairs
44: Before cleaning: 618 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44: Start terminus LYS-50: NH3+
44: End terminus PRO-65: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 232, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 618 dihedrals, 38 impropers, 419 angles
44: 597 pairs, 232 bonds and 0 virtual sites
44:
44: Total mass 1662.885 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (219 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 124 virtual sites
44: Added 16 dummy masses
44: Added 26 new constraints
44: Before cleaning: 653 pairs
44: Before cleaning: 663 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 254, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 663 dihedrals, 48 impropers, 457 angles
44: 650 pairs, 254 bonds and 130 virtual sites
44:
44: Total mass 1846.115 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (309 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 132 virtual sites
44: Added 10 dummy masses
44: Added 19 new constraints
44: Before cleaning: 748 pairs
44: Before cleaning: 778 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus PHE-33: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 290, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 778 dihedrals, 49 impropers, 516 angles
44: 736 pairs, 290 bonds and 133 virtual sites
44:
44: Total mass 2088.361 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (299 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 123 virtual sites
44: Added 22 dummy masses
44: Added 35 new constraints
44: Before cleaning: 676 pairs
44: Before cleaning: 696 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44: Start terminus ALA-34: NH3+
44: End terminus ALA-49: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 261, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 696 dihedrals, 39 impropers, 472 angles
44: 667 pairs, 261 bonds and 132 virtual sites
44:
44: Total mass 1861.130 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (328 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 111 virtual sites
44: Added 18 dummy masses
44: Added 31 new constraints
44: Before cleaning: 603 pairs
44: Before cleaning: 618 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44: Start terminus LYS-50: NH3+
44: End terminus PRO-65: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 232, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 618 dihedrals, 38 impropers, 419 angles
44: 597 pairs, 232 bonds and 116 virtual sites
44:
44: Total mass 1662.885 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (249 ms)
44: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (2109 ms total)
44:
44: [----------] 8 tests from ChainSep/Pdb2gmxTest
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 651 pairs
44: Before cleaning: 661 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44: Start terminus PHE-6: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 258 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 258, now 258
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 10 cmap torsion pairs
44:
44: There are 661 dihedrals, 46 impropers, 463 angles
44: 648 pairs, 258 bonds and 0 virtual sites
44:
44: Total mass 1882.146 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (262 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 123 pairs
44: Before cleaning: 123 dihedrals
44: Keeping all generated dihedrals
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 10 donors and 7 acceptors were found.
44: There are 7 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS8
44: NE223
44: MET12 SD55 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 317 pairs
44: Before cleaning: 322 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 4 28
44:
44: 2 'B' 7 58
44:
44: 3 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (28 atoms, 4 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 51 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 50, now 50
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 123 dihedrals, 9 impropers, 88 angles
44: 123 pairs, 50 bonds and 0 virtual sites
44:
44: Total mass 434.421 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (58 atoms, 7 residues)
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus PHE-6: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 7 residues with 124 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 125, now 125
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 5 cmap torsion pairs
44:
44: There are 322 dihedrals, 19 impropers, 227 angles
44: 314 pairs, 125 bonds and 0 virtual sites
44:
44: Total mass 846.083 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 51 atoms 4 residues
44:
44: Including chain 2 in system: 124 atoms 7 residues
44:
44: Including chain 3 in system: 83 atoms 5 residues
44:
44: Now there are 258 atoms and 16 residues
44:
44: Total mass in system 1882.146 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (162 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 651 pairs
44: Before cleaning: 661 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ILE-9: COO-
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 258 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 258, now 258
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 10 cmap torsion pairs
44:
44: There are 661 dihedrals, 46 impropers, 463 angles
44: 648 pairs, 258 bonds and 0 virtual sites
44:
44: Total mass 1882.146 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (249 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 10 donors and 12 acceptors were found.
44: There are 13 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3
44: SG9
44: HIS8 NE251 1.055
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 288 pairs
44: Before cleaning: 293 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 152 pairs
44: Before cleaning: 152 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 8 61
44:
44: 2 'B' 3 25
44:
44: 3 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (61 atoms, 8 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ILE-9: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 8 residues with 114 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 115, now 115
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6 cmap torsion pairs
44:
44: There are 293 dihedrals, 23 impropers, 203 angles
44: 285 pairs, 115 bonds and 0 virtual sites
44:
44: Total mass 888.952 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (25 atoms, 3 residues)
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 61 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 60, now 60
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 152 dihedrals, 5 impropers, 112 angles
44: 152 pairs, 60 bonds and 0 virtual sites
44:
44: Total mass 391.552 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 114 atoms 8 residues
44:
44: Including chain 2 in system: 61 atoms 3 residues
44:
44: Including chain 3 in system: 83 atoms 5 residues
44:
44: Now there are 258 atoms and 16 residues
44:
44: Total mass in system 1882.146 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (142 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 650 pairs
44: Before cleaning: 660 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Merged chains into joint molecule definitions at 3 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44: Start terminus PHE-6: NH3+
44: End terminus ILE-9: COO-
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 261 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 260, now 260
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 8 cmap torsion pairs
44:
44: There are 660 dihedrals, 45 impropers, 466 angles
44: 647 pairs, 260 bonds and 0 virtual sites
44:
44: Total mass 1900.162 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (276 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 123 pairs
44: Before cleaning: 123 dihedrals
44: Keeping all generated dihedrals
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 6 donors and 4 acceptors were found.
44: There are 3 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 164 pairs
44: Before cleaning: 169 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 152 pairs
44: Before cleaning: 152 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 4 28
44:
44: 2 'B' 4 33
44:
44: 3 'B' 3 25
44:
44: 4 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (28 atoms, 4 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 51 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 50, now 50
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 123 dihedrals, 9 impropers, 88 angles
44: 123 pairs, 50 bonds and 0 virtual sites
44:
44: Total mass 434.421 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (33 atoms, 4 residues)
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44: Start terminus PHE-6: NH3+
44: End terminus ILE-9: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 66 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 67, now 67
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 169 dihedrals, 13 impropers, 118 angles
44: 161 pairs, 67 bonds and 0 virtual sites
44:
44: Total mass 472.547 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'B' (25 atoms, 3 residues)
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 61 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 60, now 60
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 152 dihedrals, 5 impropers, 112 angles
44: 152 pairs, 60 bonds and 0 virtual sites
44:
44: Total mass 391.552 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 4 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 51 atoms 4 residues
44:
44: Including chain 2 in system: 66 atoms 4 residues
44:
44: Including chain 3 in system: 61 atoms 3 residues
44:
44: Including chain 4 in system: 83 atoms 5 residues
44:
44: Now there are 261 atoms and 16 residues
44:
44: Total mass in system 1900.162 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (153 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 652 pairs
44: Before cleaning: 662 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: Merged chains into joint molecule definitions at 1 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 256, now 256
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 12 cmap torsion pairs
44:
44: There are 662 dihedrals, 47 impropers, 460 angles
44: 649 pairs, 256 bonds and 0 virtual sites
44:
44: Total mass 1864.131 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (238 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 14 donors and 15 acceptors were found.
44: There are 20 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 441 pairs
44: Before cleaning: 446 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 11 86
44:
44: 2 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (86 atoms, 11 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 11 residues with 172 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 173, now 173
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 9 cmap torsion pairs
44:
44: There are 446 dihedrals, 29 impropers, 312 angles
44: 438 pairs, 173 bonds and 0 virtual sites
44:
44: Total mass 1262.488 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 172 atoms 11 residues
44:
44: Including chain 2 in system: 83 atoms 5 residues
44:
44: Now there are 255 atoms and 16 residues
44:
44: Total mass in system 1864.131 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (156 ms)
44: [----------] 8 tests from ChainSep/Pdb2gmxTest (1644 ms total)
44:
44: [----------] 4 tests from ChainChanges/Pdb2gmxTest
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (102 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (116 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (96 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge -0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (94 ms)
44: [----------] 4 tests from ChainChanges/Pdb2gmxTest (408 ms total)
44:
44: [----------] 4 tests from ForCharmm27CyclicSystem/Pdb2gmxTest
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: WARNING: all CONECT records are ignored
44: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 6040 pairs
44: Before cleaning: 6605 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 6040 pairs
44: Before cleaning: 6605 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb...
44: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: Moved all the water blocks to the end
44:
44: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms
44:
44: chain #res #atoms
44:
44: 1 'P' 71 1527
44:
44: 2 'Q' 71 1527
44:
44: 3 'Q' 7 7
44:
44: 4 ' ' 10 10 (only water)
44:
44: 5 ' ' 16 16 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'P' (1527 atoms, 71 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 71 residues with 2297 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 2481, now 2481
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6605 dihedrals, 183 impropers, 4434 angles
44: 5827 pairs, 2481 bonds and 0 virtual sites
44:
44: Total mass 22984.514 a.m.u.
44:
44: Total charge -71.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'Q' (1527 atoms, 71 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 71 residues with 2297 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 2481, now 2481
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6605 dihedrals, 183 impropers, 4434 angles
44: 5827 pairs, 2481 bonds and 0 virtual sites
44:
44: Total mass 22984.514 a.m.u.
44:
44: Total charge -71.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'Q' (7 atoms, 7 residues)
44:
44: Residue MG72 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG73 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG74 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG75 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG76 has type 'Ion', assuming it is not linked into a chain.
44:
44: Disabling further notes about ions.
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 7 residues with 7 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: No bonds
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 0 angles
44: 0 pairs, 0 bonds and 0 virtual sites
44:
44: Total mass 170.135 a.m.u.
44:
44: Total charge 14.000 e
44:
44: Writing topology
44:
44: Processing chain 4 (10 atoms, 10 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 10 residues with 30 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 30, now 30
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 30 angles
44: 0 pairs, 30 bonds and 0 virtual sites
44:
44: Total mass 180.154 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Processing chain 5 (16 atoms, 16 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 48 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 48, now 48
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 48 angles
44: 0 pairs, 48 bonds and 0 virtual sites
44:
44: Total mass 288.246 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Including chain 1 in system: 2297 atoms 71 residues
44:
44: Including chain 2 in system: 2297 atoms 71 residues
44:
44: Including chain 3 in system: 7 atoms 7 residues
44:
44: Including chain 4 in system: 30 atoms 10 residues
44:
44: Including chain 5 in system: 48 atoms 16 residues
44:
44: Now there are 4679 atoms and 175 residues
44:
44: Total mass in system 46607.562 a.m.u.
44:
44: Total charge in system -128.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/0 (16674 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 2325 pairs
44: Before cleaning: 2325 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb...
44: Read 'CARNOCYCLIN-A', 413 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 60 413
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (413 atoms, 60 residues)
44:
44: Identified residue LEU1 as a starting terminus.
44:
44: Identified residue LEU60 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 60 residues with 878 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 880, now 880
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 59 cmap torsion pairs
44:
44: There are 2325 dihedrals, 137 impropers, 1614 angles
44: 2319 pairs, 880 bonds and 0 virtual sites
44:
44: Total mass 5866.087 a.m.u.
44:
44: Total charge 4.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/1 (1468 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: WARNING: all CONECT records are ignored
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 12080 pairs
44: Before cleaning: 13210 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb...
44: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Moved all the water blocks to the end
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms
44:
44: chain #res #atoms
44:
44: 1 'P' 149 3061
44:
44: 2 ' ' 10 10 (only water)
44:
44: 3 ' ' 16 16 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'P' (3061 atoms, 149 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Residue MG72 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG73 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG74 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG75 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG76 has type 'Ion', assuming it is not linked into a chain.
44:
44: Disabling further notes about ions.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 149 residues with 4601 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 4962, now 4962
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 13210 dihedrals, 366 impropers, 8868 angles
44: 11654 pairs, 4962 bonds and 0 virtual sites
44:
44: Total mass 46139.162 a.m.u.
44:
44: Total charge -128.000 e
44:
44: Writing topology
44:
44: Processing chain 2 (10 atoms, 10 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 10 residues with 30 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 30, now 30
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 30 angles
44: 0 pairs, 30 bonds and 0 virtual sites
44:
44: Total mass 180.154 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Processing chain 3 (16 atoms, 16 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 48 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 48, now 48
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 48 angles
44: 0 pairs, 48 bonds and 0 virtual sites
44:
44: Total mass 288.246 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Including chain 1 in system: 4601 atoms 149 residues
44:
44: Including chain 2 in system: 30 atoms 10 residues
44:
44: Including chain 3 in system: 48 atoms 16 residues
44:
44: Now there are 4679 atoms and 175 residues
44:
44: Total mass in system 46607.562 a.m.u.
44:
44: Total charge in system -128.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/2 (35827 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 2325 pairs
44: Before cleaning: 2325 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb...
44: Read 'CARNOCYCLIN-A', 413 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 60 413
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (413 atoms, 60 residues)
44:
44: Identified residue LEU1 as a starting terminus.
44:
44: Identified residue LEU60 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 60 residues with 878 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 880, now 880
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 59 cmap torsion pairs
44:
44: There are 2325 dihedrals, 137 impropers, 1614 angles
44: 2319 pairs, 880 bonds and 0 virtual sites
44:
44: Total mass 5866.087 a.m.u.
44:
44: Total charge 4.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/3 (1410 ms)
44: [----------] 4 tests from ForCharmm27CyclicSystem/Pdb2gmxTest (55380 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 33 tests from 6 test cases ran. (61799 ms total)
44: [ PASSED ] 33 tests.
44/65 Test #44: Pdb2gmx3Test .......................... Passed 61.84 sec
test 45
Start 45: CorrelationsTest
45: Test command: /<<PKGBUILDDIR>>/build/basic/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CorrelationsTest.xml"
45: Test timeout computed to be: 30
45: [==========] Running 21 tests from 3 test cases.
45: [----------] Global test environment set-up.
45: [----------] 10 tests from AutocorrTest
45: [ RUN ] AutocorrTest.EacNormal
45: [ OK ] AutocorrTest.EacNormal (12 ms)
45: [ RUN ] AutocorrTest.EacNoNormalize
45: [ OK ] AutocorrTest.EacNoNormalize (9 ms)
45: [ RUN ] AutocorrTest.EacCos
45: [ OK ] AutocorrTest.EacCos (14 ms)
45: [ RUN ] AutocorrTest.EacVector
45: [ OK ] AutocorrTest.EacVector (19 ms)
45: [ RUN ] AutocorrTest.EacRcross
45: [ OK ] AutocorrTest.EacRcross (4 ms)
45: [ RUN ] AutocorrTest.EacP0
45: [ OK ] AutocorrTest.EacP0 (19 ms)
45: [ RUN ] AutocorrTest.EacP1
45: [ OK ] AutocorrTest.EacP1 (25 ms)
45: [ RUN ] AutocorrTest.EacP2
45: [ OK ] AutocorrTest.EacP2 (47 ms)
45: [ RUN ] AutocorrTest.EacP3
45: [ OK ] AutocorrTest.EacP3 (13 ms)
45: [ RUN ] AutocorrTest.EacP4
45: [ OK ] AutocorrTest.EacP4 (22 ms)
45: [----------] 10 tests from AutocorrTest (188 ms total)
45:
45: [----------] 10 tests from ExpfitTest
45: [ RUN ] ExpfitTest.EffnEXP1
45: [ OK ] ExpfitTest.EffnEXP1 (7 ms)
45: [ RUN ] ExpfitTest.EffnEXP2
45: [ OK ] ExpfitTest.EffnEXP2 (2 ms)
45: [ RUN ] ExpfitTest.EffnEXPEXP
45: [ OK ] ExpfitTest.EffnEXPEXP (4 ms)
45: [ RUN ] ExpfitTest.EffnEXP5
45: [ OK ] ExpfitTest.EffnEXP5 (13 ms)
45: [ RUN ] ExpfitTest.EffnEXP7
45: [ OK ] ExpfitTest.EffnEXP7 (9 ms)
45: [ RUN ] ExpfitTest.EffnEXP9
45: [ OK ] ExpfitTest.EffnEXP9 (75 ms)
45: [ RUN ] ExpfitTest.EffnERF
45: [ OK ] ExpfitTest.EffnERF (8 ms)
45: [ RUN ] ExpfitTest.EffnERREST
45: [ OK ] ExpfitTest.EffnERREST (10 ms)
45: [ RUN ] ExpfitTest.EffnVAC
45: [ OK ] ExpfitTest.EffnVAC (19 ms)
45: [ RUN ] ExpfitTest.EffnPRES
45: [ OK ] ExpfitTest.EffnPRES (52 ms)
45: [----------] 10 tests from ExpfitTest (199 ms total)
45:
45: [----------] 1 test from ManyAutocorrelationTest
45: [ RUN ] ManyAutocorrelationTest.Empty
45: [ OK ] ManyAutocorrelationTest.Empty (0 ms)
45: [----------] 1 test from ManyAutocorrelationTest (0 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 21 tests from 3 test cases ran. (417 ms total)
45: [ PASSED ] 21 tests.
45/65 Test #45: CorrelationsTest ...................... Passed 0.45 sec
test 46
Start 46: AnalysisDataUnitTests
46: Test command: /<<PKGBUILDDIR>>/build/basic/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml"
46: Test timeout computed to be: 30
46: [==========] Running 69 tests from 14 test cases.
46: [----------] Global test environment set-up.
46: [----------] 3 tests from AnalysisDataInitializationTest
46: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
46: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
46: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
46: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms)
46: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
46: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
46: [----------] 3 tests from AnalysisDataInitializationTest (1 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
46: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms)
46: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms)
46: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/0 (9 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
46: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms)
46: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (1 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (1 ms)
46: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (1 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/1 (11 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
46: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms)
46: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (1 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (1 ms)
46: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (1 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/2 (12 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
46: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (3 ms)
46: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (2 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (1 ms)
46: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (1 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/3 (14 ms total)
46:
46: [----------] 4 tests from AnalysisArrayDataTest
46: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
46: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (1 ms)
46: [ RUN ] AnalysisArrayDataTest.StorageWorks
46: [ OK ] AnalysisArrayDataTest.StorageWorks (1 ms)
46: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
46: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
46: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
46: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
46: [----------] 4 tests from AnalysisArrayDataTest (4 ms total)
46:
46: [----------] 6 tests from AverageModuleTest
46: [ RUN ] AverageModuleTest.BasicTest
46: [ OK ] AverageModuleTest.BasicTest (93 ms)
46: [ RUN ] AverageModuleTest.HandlesMultipointData
46: [ OK ] AverageModuleTest.HandlesMultipointData (6 ms)
46: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
46: [ OK ] AverageModuleTest.HandlesMultipleDataSets (4 ms)
46: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
46: [ OK ] AverageModuleTest.HandlesDataSetAveraging (3 ms)
46: [ RUN ] AverageModuleTest.CanCustomizeXAxis
46: [ OK ] AverageModuleTest.CanCustomizeXAxis (2 ms)
46: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
46: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (2 ms)
46: [----------] 6 tests from AverageModuleTest (110 ms total)
46:
46: [----------] 2 tests from FrameAverageModuleTest
46: [ RUN ] FrameAverageModuleTest.BasicTest
46: [ OK ] FrameAverageModuleTest.BasicTest (2 ms)
46: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
46: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (3 ms)
46: [----------] 2 tests from FrameAverageModuleTest (5 ms total)
46:
46: [----------] 7 tests from AnalysisHistogramSettingsTest
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
46: [----------] 7 tests from AnalysisHistogramSettingsTest (1 ms total)
46:
46: [----------] 2 tests from SimpleHistogramModuleTest
46: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
46: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (4 ms)
46: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
46: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (3 ms)
46: [----------] 2 tests from SimpleHistogramModuleTest (7 ms total)
46:
46: [----------] 3 tests from WeightedHistogramModuleTest
46: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
46: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (3 ms)
46: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
46: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (4 ms)
46: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
46: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (4 ms)
46: [----------] 3 tests from WeightedHistogramModuleTest (11 ms total)
46:
46: [----------] 3 tests from BinAverageModuleTest
46: [ RUN ] BinAverageModuleTest.ComputesCorrectly
46: [ OK ] BinAverageModuleTest.ComputesCorrectly (3 ms)
46: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
46: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (3 ms)
46: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
46: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (3 ms)
46: [----------] 3 tests from BinAverageModuleTest (9 ms total)
46:
46: [----------] 4 tests from AbstractAverageHistogramTest
46: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
46: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (4 ms)
46: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
46: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (3 ms)
46: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
46: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (3 ms)
46: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
46: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (3 ms)
46: [----------] 4 tests from AbstractAverageHistogramTest (14 ms total)
46:
46: [----------] 3 tests from LifetimeModuleTest
46: [ RUN ] LifetimeModuleTest.BasicTest
46: [ OK ] LifetimeModuleTest.BasicTest (2 ms)
46: [ RUN ] LifetimeModuleTest.CumulativeTest
46: [ OK ] LifetimeModuleTest.CumulativeTest (2 ms)
46: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
46: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (3 ms)
46: [----------] 3 tests from LifetimeModuleTest (7 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 69 tests from 14 test cases ran. (218 ms total)
46: [ PASSED ] 69 tests.
46/65 Test #46: AnalysisDataUnitTests ................. Passed 0.26 sec
test 47
Start 47: CoordinateIOTests
47: Test command: /<<PKGBUILDDIR>>/build/basic/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CoordinateIOTests.xml"
47: Test timeout computed to be: 30
47: [==========] Running 64 tests from 19 test cases.
47: [----------] Global test environment set-up.
47: [----------] 1 test from OutputSelectorDeathTest
47: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (23 ms)
47: [----------] 1 test from OutputSelectorDeathTest (23 ms total)
47:
47: [----------] 5 tests from TrajectoryFrameWriterTest
47: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (15 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (15 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (15 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (26 ms)
47: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
47: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms)
47: [----------] 5 tests from TrajectoryFrameWriterTest (72 ms total)
47:
47: [----------] 5 tests from OutputAdapterContainer
47: [ RUN ] OutputAdapterContainer.MakeEmpty
47: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
47: [ RUN ] OutputAdapterContainer.AddAdapter
47: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.RejectBadAdapter
47: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
47: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
47: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
47: [----------] 5 tests from OutputAdapterContainer (1 ms total)
47:
47: [----------] 5 tests from FlagTest
47: [ RUN ] FlagTest.CanSetSimpleFlag
47: [ OK ] FlagTest.CanSetSimpleFlag (0 ms)
47: [ RUN ] FlagTest.CanAddNewBox
47: [ OK ] FlagTest.CanAddNewBox (0 ms)
47: [ RUN ] FlagTest.SetsImplicitPrecisionChange
47: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
47: [ RUN ] FlagTest.SetsImplicitStartTimeChange
47: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
47: [ RUN ] FlagTest.SetsImplicitTimeStepChange
47: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
47: [----------] 5 tests from FlagTest (1 ms total)
47:
47: [----------] 5 tests from SetAtomsTest
47: [ RUN ] SetAtomsTest.RemovesExistingAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.RemovesExistingAtoms (12 ms)
47: [ RUN ] SetAtomsTest.AddsNewAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.AddsNewAtoms (11 ms)
47: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (12 ms)
47: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (11 ms)
47: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (12 ms)
47: [----------] 5 tests from SetAtomsTest (58 ms total)
47:
47: [----------] 2 tests from SetBothTimeTest
47: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
47: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
47: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
47: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
47: [----------] 2 tests from SetBothTimeTest (0 ms total)
47:
47: [----------] 2 tests from SetStartTimeTest
47: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
47: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
47: [ RUN ] SetStartTimeTest.WorksWithZeroStart
47: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms)
47: [----------] 2 tests from SetStartTimeTest (0 ms total)
47:
47: [----------] 1 test from SetTimeStepTest
47: [ RUN ] SetTimeStepTest.SetTimeStepWorks
47: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
47: [----------] 1 test from SetTimeStepTest (0 ms total)
47:
47: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (11 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (11 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (11 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (11 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (11 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (11 ms)
47: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (69 ms total)
47:
47: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (11 ms)
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (12 ms)
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (11 ms)
47: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (35 ms total)
47:
47: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
47: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total)
47:
47: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (23 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (23 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (24 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (23 ms)
47: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (93 ms total)
47:
47: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (12 ms)
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (11 ms)
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (11 ms)
47: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (35 ms total)
47:
47: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (1 ms)
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
47: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (1 ms total)
47:
47: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
47: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (12 ms)
47: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (11 ms)
47: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (24 ms total)
47:
47: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
47: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
47:
47: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
47: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (11 ms)
47: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (11 ms)
47: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (23 ms total)
47:
47: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms)
47: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total)
47:
47: [----------] 4 tests from ModuleSupported/NoOptionalOutput
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (12 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (11 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (11 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (11 ms)
47: [----------] 4 tests from ModuleSupported/NoOptionalOutput (47 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 64 tests from 19 test cases ran. (488 ms total)
47: [ PASSED ] 64 tests.
47/65 Test #47: CoordinateIOTests ..................... Passed 0.53 sec
test 48
Start 48: TrajectoryAnalysisUnitTests
48: Test command: /<<PKGBUILDDIR>>/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
48: Test timeout computed to be: 1920
48: [==========] Running 82 tests from 16 test cases.
48: [----------] Global test environment set-up.
48: [----------] 11 tests from AngleModuleTest
48: [ RUN ] AngleModuleTest.ComputesSimpleAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesSimpleAngles (77 ms)
48: [ RUN ] AngleModuleTest.ComputesDihedrals
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesDihedrals (9 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorPairAngles (9 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (9 ms)
48: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (8 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (8 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
48: Reading frames from gro file 'Test system for different angles', 33 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (13 ms)
48: [ RUN ] AngleModuleTest.ComputesMultipleAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesMultipleAngles (15 ms)
48: [ RUN ] AngleModuleTest.HandlesDynamicSelections
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesDynamicSelections (9 ms)
48: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (9 ms)
48: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (10 ms)
48: [----------] 11 tests from AngleModuleTest (178 ms total)
48:
48: [----------] 5 tests from ClustsizeTest
48: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
48: There is one group in the index
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 24
48: cmid: 2, cmax: 4, max_size: 6
48: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
48: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (9 ms)
48: [ RUN ] ClustsizeTest.NoMolShortCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
48: There is one group in the index
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 24
48: cmid: 1, cmax: 6, max_size: 6
48: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
48: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (7 ms)
48: [ RUN ] ClustsizeTest.MolDefaultCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 2, cmax: 4, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (8 ms)
48: [ RUN ] ClustsizeTest.MolShortCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 1, cmax: 6, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (7 ms)
48: [ RUN ] ClustsizeTest.MolCSize
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 2, cmax: 4, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolCSize (9 ms)
48: [----------] 5 tests from ClustsizeTest (41 ms total)
48:
48: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (2 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
48: Reading frames from gro file 'Test system', 8 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (8 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
48: Reading frames from gro file 'Test system', 8 atoms.
48:
Reading frame 0 time 0.000
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (8 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms)
48: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (20 ms total)
48:
48: [----------] 4 tests from ConvertTrjModuleTest
48: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (28 ms)
48: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (26 ms)
48: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (5 ms)
48: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (6 ms)
48: [----------] 4 tests from ConvertTrjModuleTest (65 ms total)
48:
48: [----------] 3 tests from DistanceModuleTest
48: [ RUN ] DistanceModuleTest.ComputesDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2:
48: Number of samples: 5
48: Average distance: 1.43246 nm
48: Standard deviation: 0.96700 nm
48: [ OK ] DistanceModuleTest.ComputesDistances (11 ms)
48: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2:
48: Number of samples: 5
48: Average distance: 1.43246 nm
48: Standard deviation: 0.96700 nm
48: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
48: Number of samples: 4
48: Average distance: 1.81066 nm
48: Standard deviation: 0.79289 nm
48: [ OK ] DistanceModuleTest.ComputesMultipleDistances (12 ms)
48: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2 and res_cog x < 2.8:
48: Number of samples: 3
48: Average distance: 1.72076 nm
48: Standard deviation: 1.24839 nm
48: [ OK ] DistanceModuleTest.HandlesDynamicSelections (12 ms)
48: [----------] 3 tests from DistanceModuleTest (36 ms total)
48:
48: [----------] 2 tests from ExtractClusterModuleTest
48: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
48: trr version: GMX_trn_file (single precision)
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
48: Analyzed 26 frames, last time 0.050
48: There are 8 clusters containing 26 structures, highest framenr is 25
48: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (11 ms)
48: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
48: Analyzed 26 frames, last time 0.050
48: There are 8 clusters containing 26 structures, highest framenr is 25
48: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (9 ms)
48: [----------] 2 tests from ExtractClusterModuleTest (21 ms total)
48:
48: [----------] 2 tests from FreeVolumeModuleTest
48: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for 40 particles. These were set to zero.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: cutoff = 0.18 nm
48: probe_radius = 0 nm
48: seed = 13
48: ninsert = 1000 probes per nm^3
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
48: van der Spoel and Luciano T. Costa
48: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
48: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
48: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
48: -------- -------- --- Thank You --- -------- --------
48:
48: Free volume 38.02 +/- 0.00 %
48: Total volume 68.92 +/- 0.00 nm^3
48: Number of molecules 340 total mass 63491.38 Dalton
48: Average molar mass: 186.74 Dalton
48: Density rho: 1529.71 +/- 0.00 nm^3
48: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
48: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
48: Fractional free volume 0.194 +/- 0.000
48: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (320 ms)
48: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: cutoff = 0.18 nm
48: probe_radius = 0 nm
48: seed = 17
48: ninsert = 1000 probes per nm^3
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
48: van der Spoel and Luciano T. Costa
48: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
48: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
48: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
48: -------- -------- --- Thank You --- -------- --------
48:
48: Free volume 38.48 +/- 0.00 %
48: Total volume 68.92 +/- 0.00 nm^3
48: Number of molecules 340 total mass 63491.38 Dalton
48: Average molar mass: 186.74 Dalton
48: Density rho: 1529.71 +/- 0.00 nm^3
48: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
48: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
48: Fractional free volume 0.200 +/- 0.000
48: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (304 ms)
48: [----------] 2 tests from FreeVolumeModuleTest (624 ms total)
48:
48: [----------] 9 tests from PairDistanceModuleTest
48: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesAllDistances (9 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (9 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (8 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (8 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (9 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (9 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (9 ms)
48: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (8 ms)
48: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (9 ms)
48: [----------] 9 tests from PairDistanceModuleTest (79 ms total)
48:
48: [----------] 5 tests from RdfModuleTest
48: [ RUN ] RdfModuleTest.BasicTest
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.BasicTest (149 ms)
48: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
48: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (47 ms)
48: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (72 ms)
48: [ RUN ] RdfModuleTest.CalculatesSurf
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.CalculatesSurf (45 ms)
48: [ RUN ] RdfModuleTest.CalculatesXY
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.CalculatesXY (82 ms)
48: [----------] 5 tests from RdfModuleTest (397 ms total)
48:
48: [----------] 5 tests from SasaModuleTest
48: [ RUN ] SasaModuleTest.BasicTest
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.BasicTest (38 ms)
48: [ RUN ] SasaModuleTest.HandlesSelectedResidues
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesSelectedResidues (24 ms)
48: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (21 ms)
48: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (31 ms)
48: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (35 ms)
48: [----------] 5 tests from SasaModuleTest (153 ms total)
48:
48: [----------] 8 tests from SelectModuleTest
48: [ RUN ] SelectModuleTest.BasicTest
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.BasicTest (22 ms)
48: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (17 ms)
48: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (18 ms)
48: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (17 ms)
48: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (46 ms)
48: [ RUN ] SelectModuleTest.NormalizesSizes
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.NormalizesSizes (10 ms)
48: [ RUN ] SelectModuleTest.WritesResidueNumbers
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.WritesResidueNumbers (10 ms)
48: [ RUN ] SelectModuleTest.WritesResidueIndices
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.WritesResidueIndices (11 ms)
48: [----------] 8 tests from SelectModuleTest (153 ms total)
48:
48: [----------] 10 tests from SurfaceAreaTest
48: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
48: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
48: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
48: [ OK ] SurfaceAreaTest.ComputesTwoPoints (3 ms)
48: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
48: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (3 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints12
48: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints32
48: [ OK ] SurfaceAreaTest.SurfacePoints32 (2 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints42
48: [ OK ] SurfaceAreaTest.SurfacePoints42 (3 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints122
48: [ OK ] SurfaceAreaTest.SurfacePoints122 (4 ms)
48: [ RUN ] SurfaceAreaTest.Computes100Points
48: [ OK ] SurfaceAreaTest.Computes100Points (3 ms)
48: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
48: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (9 ms)
48: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
48: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (10 ms)
48: [----------] 10 tests from SurfaceAreaTest (40 ms total)
48:
48: [----------] 4 tests from TopologyInformation
48: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
48: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
48: [ RUN ] TopologyInformation.WorksWithGroFile
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TopologyInformation.WorksWithGroFile (15 ms)
48: [ RUN ] TopologyInformation.WorksWithPdbFile
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TopologyInformation.WorksWithPdbFile (16 ms)
48: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Generating 1-4 interactions: fudge = 0.5
48:
48: NOTE 2 [file lysozyme.top, line 1465]:
48: System has non-zero total charge: 2.000000
48: Total charge should normally be an integer. See
48: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
48: for discussion on how close it should be to an integer.
48:
48:
48:
48: Number of degrees of freedom in T-Coupling group rest is 465.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
48: Setting the LD random seed to 591134127
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48:
48: Generated 330891 of the 330891 1-4 parameter combinations
48:
48: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
48: Analysing residue names:
48: There are: 10 Protein residues
48: Analysing Protein...
48:
48: This run will generate roughly 0 Mb of data
48: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (2115 ms)
48: [----------] 4 tests from TopologyInformation (2149 ms total)
48:
48: [----------] 4 tests from TrajectoryModuleTest
48: [ RUN ] TrajectoryModuleTest.BasicTest
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.BasicTest (83 ms)
48: [ RUN ] TrajectoryModuleTest.PlotsXOnly
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.PlotsXOnly (22 ms)
48: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (15 ms)
48: [ RUN ] TrajectoryModuleTest.HandlesNoForces
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.HandlesNoForces (15 ms)
48: [----------] 4 tests from TrajectoryModuleTest (148 ms total)
48:
48: [----------] 5 tests from UnionFinderTest
48: [ RUN ] UnionFinderTest.WorksEmpty
48: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
48: [ RUN ] UnionFinderTest.BasicMerges
48: [ OK ] UnionFinderTest.BasicMerges (0 ms)
48: [ RUN ] UnionFinderTest.LargerMerges
48: [ OK ] UnionFinderTest.LargerMerges (0 ms)
48: [ RUN ] UnionFinderTest.LongRightMerge
48: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
48: [ RUN ] UnionFinderTest.LongLeftMerge
48: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
48: [----------] 5 tests from UnionFinderTest (1 ms total)
48:
48: [----------] 1 test from MappedUnionFinderTest
48: [ RUN ] MappedUnionFinderTest.BasicMerges
48: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
48: [----------] 1 test from MappedUnionFinderTest (0 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 82 tests from 16 test cases ran. (4106 ms total)
48: [ PASSED ] 82 tests.
48/65 Test #48: TrajectoryAnalysisUnitTests ........... Passed 4.16 sec
test 49
Start 49: EnergyAnalysisUnitTests
49: Test command: /<<PKGBUILDDIR>>/build/basic/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml"
49: Test timeout computed to be: 30
49: [==========] Running 7 tests from 4 test cases.
49: [----------] Global test environment set-up.
49: [----------] 1 test from DhdlTest
49: [ RUN ] DhdlTest.ExtractDhdl
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
49: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
49: Note: file tpx version 110, software tpx version 122
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
49:
49:
49: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
49: [ OK ] DhdlTest.ExtractDhdl (70 ms)
49: [----------] 1 test from DhdlTest (72 ms total)
49:
49: [----------] 1 test from OriresTest
49: [ RUN ] OriresTest.ExtractOrires
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
49: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
49: Note: file tpx version 111, software tpx version 122
49: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
49: End your selection with 0
49: Selecting all 7 orientation restraints
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
49: [ OK ] OriresTest.ExtractOrires (53 ms)
49: [----------] 1 test from OriresTest (53 ms total)
49:
49: [----------] 3 tests from EnergyTest
49: [ RUN ] EnergyTest.ExtractEnergy
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
49: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
49: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
49: [ OK ] EnergyTest.ExtractEnergy (14 ms)
49: [ RUN ] EnergyTest.ExtractEnergyByNumber
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
49: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
49: Pres. DC -268.49 3 8.52175 13.2804 (bar)
49: [ OK ] EnergyTest.ExtractEnergyByNumber (13 ms)
49: [ RUN ] EnergyTest.ExtractEnergyMixed
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: [ OK ] EnergyTest.ExtractEnergyMixed (13 ms)
49: [----------] 3 tests from EnergyTest (41 ms total)
49:
49: [----------] 2 tests from ViscosityTest
49: [ RUN ] ViscosityTest.EinsteinViscosity
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Pres-XX 20.2092 65 717.193 185.978 (bar)
49: Pres-XY -47.7351 39 372.522 207.456 (bar)
49: Pres-XZ 11.477 31 379.79 6.80818 (bar)
49: Pres-YX -47.7106 39 372.525 207.5 (bar)
49: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
49: Pres-YZ -41.3534 45 401.216 114.663 (bar)
49: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
49: Pres-ZY -41.3119 45 401.196 114.743 (bar)
49: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
49: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: [ OK ] ViscosityTest.EinsteinViscosity (28 ms)
49: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Pres-XX 20.2092 65 717.193 185.978 (bar)
49: Pres-XY -47.7351 39 372.522 207.456 (bar)
49: Pres-XZ 11.477 31 379.79 6.80818 (bar)
49: Pres-YX -47.7106 39 372.525 207.5 (bar)
49: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
49: Pres-YZ -41.3534 45 401.216 114.663 (bar)
49: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
49: Pres-ZY -41.3119 45 401.196 114.743 (bar)
49: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
49: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: [ OK ] ViscosityTest.EinsteinViscosityIntegral (28 ms)
49: [----------] 2 tests from ViscosityTest (56 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 7 tests from 4 test cases ran. (223 ms total)
49: [ PASSED ] 7 tests.
49/65 Test #49: EnergyAnalysisUnitTests ............... Passed 0.27 sec
test 50
Start 50: ToolUnitTests
50: Test command: /<<PKGBUILDDIR>>/build/basic/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ToolUnitTests.xml"
50: Test timeout computed to be: 1920
50: [==========] Running 21 tests from 5 test cases.
50: [----------] Global test environment set-up.
50: [----------] 2 tests from DumpTest
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: For a correct single-point energy evaluation with nsteps = 0, use
50: continuation = yes to avoid constraining the input coordinates.
50:
50: Generating 1-4 interactions: fudge = 0.5
50:
50: NOTE 2 [file lysozyme.top, line 1465]:
50: System has non-zero total charge: 2.000000
50: Total charge should normally be an integer. See
50: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
50: for discussion on how close it should be to an integer.
50:
50:
50:
50: Number of degrees of freedom in T-Coupling group rest is 465.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: NVE simulation with an initial temperature of zero: will use a Verlet
50: buffer of 10%. Check your energy drift!
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Setting the LD random seed to -67633298
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50:
50: Generated 330891 of the 330891 1-4 parameter combinations
50:
50: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
50: Analysing residue names:
50: There are: 10 Protein residues
50: Analysing Protein...
50:
50: This run will generate roughly 0 Mb of data
50: [ RUN ] DumpTest.WorksWithTpr
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
50: /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
50: inputrec:
50: integrator = md
50: tinit = 0
50: dt = 0.001
50: nsteps = 0
50: init-step = 0
50: simulation-part = 1
50: mts = false
50: comm-mode = Linear
50: nstcomm = 100
50: bd-fric = 0
50: ld-seed = -67633298
50: emtol = 10
50: emstep = 0.01
50: niter = 20
50: fcstep = 0
50: nstcgsteep = 1000
50: nbfgscorr = 10
50: rtpi = 0.05
50: nstxout = 0
50: nstvout = 0
50: nstfout = 0
50: nstlog = 1000
50: nstcalcenergy = 100
50: nstenergy = 1000
50: nstxout-compressed = 0
50: compressed-x-precision = 1000
50: cutoff-scheme = Verlet
50: nstlist = 10
50: pbc = xyz
50: periodic-molecules = false
50: verlet-buffer-tolerance = -1
50: rlist = 1.1
50: coulombtype = Cut-off
50: coulomb-modifier = Potential-shift
50: rcoulomb-switch = 0
50: rcoulomb = 1
50: epsilon-r = 1
50: epsilon-rf = inf
50: vdw-type = Cut-off
50: vdw-modifier = Potential-shift
50: rvdw-switch = 0
50: rvdw = 1
50: DispCorr = No
50: table-extension = 1
50: fourierspacing = 0.12
50: fourier-nx = 0
50: fourier-ny = 0
50: fourier-nz = 0
50: pme-order = 4
50: ewald-rtol = 1e-05
50: ewald-rtol-lj = 0.001
50: lj-pme-comb-rule = Geometric
50: ewald-geometry = 0
50: epsilon-surface = 0
50: tcoupl = No
50: nsttcouple = -1
50: nh-chain-length = 0
50: print-nose-hoover-chain-variables = false
50: pcoupl = No
50: pcoupltype = Isotropic
50: nstpcouple = -1
50: tau-p = 1
50: compressibility (3x3):
50: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p (3x3):
50: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: refcoord-scaling = No
50: posres-com (3):
50: posres-com[0]= 0.00000e+00
50: posres-com[1]= 0.00000e+00
50: posres-com[2]= 0.00000e+00
50: posres-comB (3):
50: posres-comB[0]= 0.00000e+00
50: posres-comB[1]= 0.00000e+00
50: posres-comB[2]= 0.00000e+00
50: QMMM = false
50: qm-opts:
50: ngQM = 0
50: constraint-algorithm = Lincs
50: continuation = false
50: Shake-SOR = false
50: shake-tol = 0.0001
50: lincs-order = 4
50: lincs-iter = 1
50: lincs-warnangle = 30
50: nwall = 0
50: wall-type = 9-3
50: wall-r-linpot = -1
50: wall-atomtype[0] = -1
50: wall-atomtype[1] = -1
50: wall-density[0] = 0
50: wall-density[1] = 0
50: wall-ewald-zfac = 3
50: pull = false
50: awh = false
50: rotation = false
50: interactiveMD = false
50: disre = No
50: disre-weighting = Conservative
50: disre-mixed = false
50: dr-fc = 1000
50: dr-tau = 0
50: nstdisreout = 100
50: orire-fc = 0
50: orire-tau = 0
50: nstorireout = 100
50: free-energy = no
50: cos-acceleration = 0
50: deform (3x3):
50: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: simulated-tempering = false
50: swapcoords = no
50: userint1 = 0
50: userint2 = 0
50: userint3 = 0
50: userint4 = 0
50: userreal1 = 0
50: userreal2 = 0
50: userreal3 = 0
50: userreal4 = 0
50: applied-forces:
50: electric-field:
50: x:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: y:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: z:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: density-guided-simulation:
50: active = false
50: group = protein
50: similarity-measure = inner-product
50: atom-spreading-weight = unity
50: force-constant = 1e+09
50: gaussian-transform-spreading-width = 0.2
50: gaussian-transform-spreading-range-in-multiples-of-width = 4
50: reference-density-filename = reference.mrc
50: nst = 1
50: normalize-densities = true
50: adaptive-force-scaling = false
50: adaptive-force-scaling-time-constant = 4
50: shift-vector =
50: transformation-matrix =
50: grpopts:
50: nrdf: 465
50: ref-t: 0
50: tau-t: 0
50: annealing: No
50: annealing-npoints: 0
50: acc: 0 0 0
50: nfreeze: N N N
50: energygrp-flags[ 0]: 0
50: header:
50: bIr = present
50: bBox = present
50: bTop = present
50: bX = present
50: bV = present
50: bF = not present
50: natoms = 156
50: lambda = 0.000000e+00
50: buffer size = 59458
50: topology:
50: name="First 10 residues from 1AKI"
50: #atoms = 156
50: #molblock = 1
50: molblock (0):
50: moltype = 0 "Protein_chain_B"
50: #molecules = 1
50: #posres_xA = 0
50: #posres_xB = 0
50: bIntermolecularInteractions = false
50: ffparams:
50: atnr=10
50: ntypes=212
50: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06
50: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
50: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
50: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
50: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
50: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
50: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
50: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
50: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
50: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
50: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06
50: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
50: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
50: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
50: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
50: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
50: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
50: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
50: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
50: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
50: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08
50: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
50: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
50: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
50: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
50: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
50: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
50: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
50: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
50: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
50: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05
50: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
50: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
50: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
50: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
50: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
50: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
50: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
50: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
50: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
50: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06
50: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
50: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
50: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
50: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
50: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
50: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
50: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
50: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
50: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
50: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06
50: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
50: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
50: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
50: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
50: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
50: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
50: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
50: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
50: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
50: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08
50: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
50: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
50: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
50: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
50: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
50: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
50: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
50: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
50: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
50: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08
50: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
50: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
50: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
50: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
50: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
50: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
50: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
50: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
50: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
50: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05
50: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
50: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
50: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
50: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
50: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
50: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
50: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
50: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
50: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
50: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
50: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
50: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
50: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
50: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
50: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
50: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
50: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
50: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
50: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
50: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
50: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
50: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
50: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
50: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
50: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
50: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
50: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
50: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
50: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
50: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
50: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
50: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
50: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
50: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
50: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
50: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
50: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
50: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
50: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
50: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
50: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2
50: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2
50: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2
50: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07
50: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06
50: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06
50: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06
50: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
50: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07
50: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06
50: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08
50: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07
50: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06
50: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07
50: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06
50: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06
50: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06
50: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06
50: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07
50: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07
50: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07
50: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06
50: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06
50: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08
50: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07
50: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08
50: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06
50: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07
50: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05
50: reppow = 12
50: fudgeQQ = 0.5
50: cmap
50: atomtypes:
50: atomtype[ 0]={atomnumber= 7}
50: atomtype[ 1]={atomnumber= 1}
50: atomtype[ 2]={atomnumber= 6}
50: atomtype[ 3]={atomnumber= 1}
50: atomtype[ 4]={atomnumber= 6}
50: atomtype[ 5]={atomnumber= 8}
50: atomtype[ 6]={atomnumber= 6}
50: atomtype[ 7]={atomnumber= 1}
50: atomtype[ 8]={atomnumber= 6}
50: atomtype[ 9]={atomnumber= 16}
50: moltype (0):
50: name="Protein_chain_B"
50: atoms:
50: atom (156):
50: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
50: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
50: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
50: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
50: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
50: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
50: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
50: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
50: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
50: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
50: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
50: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
50: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
50: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
50: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
50: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
50: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
50: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
50: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
50: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
50: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
50: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
50: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
50: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
50: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
50: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
50: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
50: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
50: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
50: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
50: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
50: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
50: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
50: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
50: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
50: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
50: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
50: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
50: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
50: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
50: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
50: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
50: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
50: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
50: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
50: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
50: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
50: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
50: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
50: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
50: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
50: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
50: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
50: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
50: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
50: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
50: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
50: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
50: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
50: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
50: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
50: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
50: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
50: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
50: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
50: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
50: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
50: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
50: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
50: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
50: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
50: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
50: atom (156):
50: atom[0]={name="N"}
50: atom[1]={name="H1"}
50: atom[2]={name="H2"}
50: atom[3]={name="H3"}
50: atom[4]={name="CA"}
50: atom[5]={name="HA"}
50: atom[6]={name="CB"}
50: atom[7]={name="HB1"}
50: atom[8]={name="HB2"}
50: atom[9]={name="CG"}
50: atom[10]={name="HG1"}
50: atom[11]={name="HG2"}
50: atom[12]={name="CD"}
50: atom[13]={name="HD1"}
50: atom[14]={name="HD2"}
50: atom[15]={name="CE"}
50: atom[16]={name="HE1"}
50: atom[17]={name="HE2"}
50: atom[18]={name="NZ"}
50: atom[19]={name="HZ1"}
50: atom[20]={name="HZ2"}
50: atom[21]={name="HZ3"}
50: atom[22]={name="C"}
50: atom[23]={name="O"}
50: atom[24]={name="N"}
50: atom[25]={name="H"}
50: atom[26]={name="CA"}
50: atom[27]={name="HA"}
50: atom[28]={name="CB"}
50: atom[29]={name="HB"}
50: atom[30]={name="CG1"}
50: atom[31]={name="HG11"}
50: atom[32]={name="HG12"}
50: atom[33]={name="HG13"}
50: atom[34]={name="CG2"}
50: atom[35]={name="HG21"}
50: atom[36]={name="HG22"}
50: atom[37]={name="HG23"}
50: atom[38]={name="C"}
50: atom[39]={name="O"}
50: atom[40]={name="N"}
50: atom[41]={name="H"}
50: atom[42]={name="CA"}
50: atom[43]={name="HA"}
50: atom[44]={name="CB"}
50: atom[45]={name="HB1"}
50: atom[46]={name="HB2"}
50: atom[47]={name="CG"}
50: atom[48]={name="CD1"}
50: atom[49]={name="HD1"}
50: atom[50]={name="CD2"}
50: atom[51]={name="HD2"}
50: atom[52]={name="CE1"}
50: atom[53]={name="HE1"}
50: atom[54]={name="CE2"}
50: atom[55]={name="HE2"}
50: atom[56]={name="CZ"}
50: atom[57]={name="HZ"}
50: atom[58]={name="C"}
50: atom[59]={name="O"}
50: atom[60]={name="N"}
50: atom[61]={name="H"}
50: atom[62]={name="CA"}
50: atom[63]={name="HA1"}
50: atom[64]={name="HA2"}
50: atom[65]={name="C"}
50: atom[66]={name="O"}
50: atom[67]={name="N"}
50: atom[68]={name="H"}
50: atom[69]={name="CA"}
50: atom[70]={name="HA"}
50: atom[71]={name="CB"}
50: atom[72]={name="HB1"}
50: atom[73]={name="HB2"}
50: atom[74]={name="CG"}
50: atom[75]={name="HG1"}
50: atom[76]={name="HG2"}
50: atom[77]={name="CD"}
50: atom[78]={name="HD1"}
50: atom[79]={name="HD2"}
50: atom[80]={name="NE"}
50: atom[81]={name="HE"}
50: atom[82]={name="CZ"}
50: atom[83]={name="NH1"}
50: atom[84]={name="HH11"}
50: atom[85]={name="HH12"}
50: atom[86]={name="NH2"}
50: atom[87]={name="HH21"}
50: atom[88]={name="HH22"}
50: atom[89]={name="C"}
50: atom[90]={name="O"}
50: atom[91]={name="N"}
50: atom[92]={name="H"}
50: atom[93]={name="CA"}
50: atom[94]={name="HA"}
50: atom[95]={name="CB"}
50: atom[96]={name="HB1"}
50: atom[97]={name="HB2"}
50: atom[98]={name="SG"}
50: atom[99]={name="HG"}
50: atom[100]={name="C"}
50: atom[101]={name="O"}
50: atom[102]={name="N"}
50: atom[103]={name="H"}
50: atom[104]={name="CA"}
50: atom[105]={name="HA"}
50: atom[106]={name="CB"}
50: atom[107]={name="HB1"}
50: atom[108]={name="HB2"}
50: atom[109]={name="CG"}
50: atom[110]={name="HG1"}
50: atom[111]={name="HG2"}
50: atom[112]={name="CD"}
50: atom[113]={name="OE1"}
50: atom[114]={name="OE2"}
50: atom[115]={name="C"}
50: atom[116]={name="O"}
50: atom[117]={name="N"}
50: atom[118]={name="H"}
50: atom[119]={name="CA"}
50: atom[120]={name="HA"}
50: atom[121]={name="CB"}
50: atom[122]={name="HB1"}
50: atom[123]={name="HB2"}
50: atom[124]={name="CG"}
50: atom[125]={name="HG"}
50: atom[126]={name="CD1"}
50: atom[127]={name="HD11"}
50: atom[128]={name="HD12"}
50: atom[129]={name="HD13"}
50: atom[130]={name="CD2"}
50: atom[131]={name="HD21"}
50: atom[132]={name="HD22"}
50: atom[133]={name="HD23"}
50: atom[134]={name="C"}
50: atom[135]={name="O"}
50: atom[136]={name="N"}
50: atom[137]={name="H"}
50: atom[138]={name="CA"}
50: atom[139]={name="HA"}
50: atom[140]={name="CB"}
50: atom[141]={name="HB1"}
50: atom[142]={name="HB2"}
50: atom[143]={name="HB3"}
50: atom[144]={name="C"}
50: atom[145]={name="O"}
50: atom[146]={name="N"}
50: atom[147]={name="H"}
50: atom[148]={name="CA"}
50: atom[149]={name="HA"}
50: atom[150]={name="CB"}
50: atom[151]={name="HB1"}
50: atom[152]={name="HB2"}
50: atom[153]={name="HB3"}
50: atom[154]={name="C"}
50: atom[155]={name="O"}
50: type (156):
50: type[0]={name="opls_287",nameB="opls_287"}
50: type[1]={name="opls_290",nameB="opls_290"}
50: type[2]={name="opls_290",nameB="opls_290"}
50: type[3]={name="opls_290",nameB="opls_290"}
50: type[4]={name="opls_293B",nameB="opls_293B"}
50: type[5]={name="opls_140",nameB="opls_140"}
50: type[6]={name="opls_136",nameB="opls_136"}
50: type[7]={name="opls_140",nameB="opls_140"}
50: type[8]={name="opls_140",nameB="opls_140"}
50: type[9]={name="opls_136",nameB="opls_136"}
50: type[10]={name="opls_140",nameB="opls_140"}
50: type[11]={name="opls_140",nameB="opls_140"}
50: type[12]={name="opls_136",nameB="opls_136"}
50: type[13]={name="opls_140",nameB="opls_140"}
50: type[14]={name="opls_140",nameB="opls_140"}
50: type[15]={name="opls_292",nameB="opls_292"}
50: type[16]={name="opls_140",nameB="opls_140"}
50: type[17]={name="opls_140",nameB="opls_140"}
50: type[18]={name="opls_287",nameB="opls_287"}
50: type[19]={name="opls_290",nameB="opls_290"}
50: type[20]={name="opls_290",nameB="opls_290"}
50: type[21]={name="opls_290",nameB="opls_290"}
50: type[22]={name="opls_235",nameB="opls_235"}
50: type[23]={name="opls_236",nameB="opls_236"}
50: type[24]={name="opls_238",nameB="opls_238"}
50: type[25]={name="opls_241",nameB="opls_241"}
50: type[26]={name="opls_224B",nameB="opls_224B"}
50: type[27]={name="opls_140",nameB="opls_140"}
50: type[28]={name="opls_137",nameB="opls_137"}
50: type[29]={name="opls_140",nameB="opls_140"}
50: type[30]={name="opls_135",nameB="opls_135"}
50: type[31]={name="opls_140",nameB="opls_140"}
50: type[32]={name="opls_140",nameB="opls_140"}
50: type[33]={name="opls_140",nameB="opls_140"}
50: type[34]={name="opls_135",nameB="opls_135"}
50: type[35]={name="opls_140",nameB="opls_140"}
50: type[36]={name="opls_140",nameB="opls_140"}
50: type[37]={name="opls_140",nameB="opls_140"}
50: type[38]={name="opls_235",nameB="opls_235"}
50: type[39]={name="opls_236",nameB="opls_236"}
50: type[40]={name="opls_238",nameB="opls_238"}
50: type[41]={name="opls_241",nameB="opls_241"}
50: type[42]={name="opls_224B",nameB="opls_224B"}
50: type[43]={name="opls_140",nameB="opls_140"}
50: type[44]={name="opls_149",nameB="opls_149"}
50: type[45]={name="opls_140",nameB="opls_140"}
50: type[46]={name="opls_140",nameB="opls_140"}
50: type[47]={name="opls_145",nameB="opls_145"}
50: type[48]={name="opls_145",nameB="opls_145"}
50: type[49]={name="opls_146",nameB="opls_146"}
50: type[50]={name="opls_145",nameB="opls_145"}
50: type[51]={name="opls_146",nameB="opls_146"}
50: type[52]={name="opls_145",nameB="opls_145"}
50: type[53]={name="opls_146",nameB="opls_146"}
50: type[54]={name="opls_145",nameB="opls_145"}
50: type[55]={name="opls_146",nameB="opls_146"}
50: type[56]={name="opls_145",nameB="opls_145"}
50: type[57]={name="opls_146",nameB="opls_146"}
50: type[58]={name="opls_235",nameB="opls_235"}
50: type[59]={name="opls_236",nameB="opls_236"}
50: type[60]={name="opls_238",nameB="opls_238"}
50: type[61]={name="opls_241",nameB="opls_241"}
50: type[62]={name="opls_223B",nameB="opls_223B"}
50: type[63]={name="opls_140",nameB="opls_140"}
50: type[64]={name="opls_140",nameB="opls_140"}
50: type[65]={name="opls_235",nameB="opls_235"}
50: type[66]={name="opls_236",nameB="opls_236"}
50: type[67]={name="opls_238",nameB="opls_238"}
50: type[68]={name="opls_241",nameB="opls_241"}
50: type[69]={name="opls_224B",nameB="opls_224B"}
50: type[70]={name="opls_140",nameB="opls_140"}
50: type[71]={name="opls_136",nameB="opls_136"}
50: type[72]={name="opls_140",nameB="opls_140"}
50: type[73]={name="opls_140",nameB="opls_140"}
50: type[74]={name="opls_308",nameB="opls_308"}
50: type[75]={name="opls_140",nameB="opls_140"}
50: type[76]={name="opls_140",nameB="opls_140"}
50: type[77]={name="opls_307",nameB="opls_307"}
50: type[78]={name="opls_140",nameB="opls_140"}
50: type[79]={name="opls_140",nameB="opls_140"}
50: type[80]={name="opls_303",nameB="opls_303"}
50: type[81]={name="opls_304",nameB="opls_304"}
50: type[82]={name="opls_302",nameB="opls_302"}
50: type[83]={name="opls_300",nameB="opls_300"}
50: type[84]={name="opls_301",nameB="opls_301"}
50: type[85]={name="opls_301",nameB="opls_301"}
50: type[86]={name="opls_300",nameB="opls_300"}
50: type[87]={name="opls_301",nameB="opls_301"}
50: type[88]={name="opls_301",nameB="opls_301"}
50: type[89]={name="opls_235",nameB="opls_235"}
50: type[90]={name="opls_236",nameB="opls_236"}
50: type[91]={name="opls_238",nameB="opls_238"}
50: type[92]={name="opls_241",nameB="opls_241"}
50: type[93]={name="opls_224B",nameB="opls_224B"}
50: type[94]={name="opls_140",nameB="opls_140"}
50: type[95]={name="opls_206",nameB="opls_206"}
50: type[96]={name="opls_140",nameB="opls_140"}
50: type[97]={name="opls_140",nameB="opls_140"}
50: type[98]={name="opls_200",nameB="opls_200"}
50: type[99]={name="opls_204",nameB="opls_204"}
50: type[100]={name="opls_235",nameB="opls_235"}
50: type[101]={name="opls_236",nameB="opls_236"}
50: type[102]={name="opls_238",nameB="opls_238"}
50: type[103]={name="opls_241",nameB="opls_241"}
50: type[104]={name="opls_224B",nameB="opls_224B"}
50: type[105]={name="opls_140",nameB="opls_140"}
50: type[106]={name="opls_136",nameB="opls_136"}
50: type[107]={name="opls_140",nameB="opls_140"}
50: type[108]={name="opls_140",nameB="opls_140"}
50: type[109]={name="opls_274",nameB="opls_274"}
50: type[110]={name="opls_140",nameB="opls_140"}
50: type[111]={name="opls_140",nameB="opls_140"}
50: type[112]={name="opls_271",nameB="opls_271"}
50: type[113]={name="opls_272",nameB="opls_272"}
50: type[114]={name="opls_272",nameB="opls_272"}
50: type[115]={name="opls_235",nameB="opls_235"}
50: type[116]={name="opls_236",nameB="opls_236"}
50: type[117]={name="opls_238",nameB="opls_238"}
50: type[118]={name="opls_241",nameB="opls_241"}
50: type[119]={name="opls_224B",nameB="opls_224B"}
50: type[120]={name="opls_140",nameB="opls_140"}
50: type[121]={name="opls_136",nameB="opls_136"}
50: type[122]={name="opls_140",nameB="opls_140"}
50: type[123]={name="opls_140",nameB="opls_140"}
50: type[124]={name="opls_137",nameB="opls_137"}
50: type[125]={name="opls_140",nameB="opls_140"}
50: type[126]={name="opls_135",nameB="opls_135"}
50: type[127]={name="opls_140",nameB="opls_140"}
50: type[128]={name="opls_140",nameB="opls_140"}
50: type[129]={name="opls_140",nameB="opls_140"}
50: type[130]={name="opls_135",nameB="opls_135"}
50: type[131]={name="opls_140",nameB="opls_140"}
50: type[132]={name="opls_140",nameB="opls_140"}
50: type[133]={name="opls_140",nameB="opls_140"}
50: type[134]={name="opls_235",nameB="opls_235"}
50: type[135]={name="opls_236",nameB="opls_236"}
50: type[136]={name="opls_238",nameB="opls_238"}
50: type[137]={name="opls_241",nameB="opls_241"}
50: type[138]={name="opls_224B",nameB="opls_224B"}
50: type[139]={name="opls_140",nameB="opls_140"}
50: type[140]={name="opls_135",nameB="opls_135"}
50: type[141]={name="opls_140",nameB="opls_140"}
50: type[142]={name="opls_140",nameB="opls_140"}
50: type[143]={name="opls_140",nameB="opls_140"}
50: type[144]={name="opls_235",nameB="opls_235"}
50: type[145]={name="opls_236",nameB="opls_236"}
50: type[146]={name="opls_238",nameB="opls_238"}
50: type[147]={name="opls_241",nameB="opls_241"}
50: type[148]={name="opls_224B",nameB="opls_224B"}
50: type[149]={name="opls_140",nameB="opls_140"}
50: type[150]={name="opls_135",nameB="opls_135"}
50: type[151]={name="opls_140",nameB="opls_140"}
50: type[152]={name="opls_140",nameB="opls_140"}
50: type[153]={name="opls_140",nameB="opls_140"}
50: type[154]={name="opls_235",nameB="opls_235"}
50: type[155]={name="opls_236",nameB="opls_236"}
50: residue (10):
50: residue[0]={name="LYS", nr=1, ic=' '}
50: residue[1]={name="VAL", nr=2, ic=' '}
50: residue[2]={name="PHE", nr=3, ic=' '}
50: residue[3]={name="GLY", nr=4, ic=' '}
50: residue[4]={name="ARG", nr=5, ic=' '}
50: residue[5]={name="CYS", nr=6, ic=' '}
50: residue[6]={name="GLU", nr=7, ic=' '}
50: residue[7]={name="LEU", nr=8, ic=' '}
50: residue[8]={name="ALA", nr=9, ic=' '}
50: residue[9]={name="ALA", nr=10, ic=' '}
50: excls:
50: numLists=156
50: numElements=1828
50: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
50: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
50: 23, 24, 25, 26}
50: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
50: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
50: 14, 15, 22, 23, 24}
50: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
50: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
50: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
50: 16, 17, 18, 22}
50: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
50: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
50: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
50: 17, 18, 19, 20, 21}
50: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
50: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
50: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
50: 20, 21}
50: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25,
50: 26, 27, 28, 38}
50: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26}
50: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
50: 30, 34, 38, 39, 40}
50: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38}
50: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
50: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
50: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
50: 40}
50: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
50: 34, 35, 36, 37, 38, 39, 40}
50: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
50: 40, 41, 42, 43, 44, 58}
50: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42}
50: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
50: 45, 46, 47, 58, 59, 60}
50: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58}
50: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
50: 48, 50, 58, 59, 60, 61, 62}
50: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
50: 60}
50: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
50: 50, 51, 52, 54, 58, 59, 60}
50: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
50: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
50: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
50: 52, 53, 54, 55, 56, 58}
50: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
50: 54, 56, 57}
50: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56}
50: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
50: 55, 56, 57}
50: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56}
50: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
50: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57}
50: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
50: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57}
50: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
50: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57}
50: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
50: 60, 61, 62, 63, 64, 65}
50: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62}
50: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
50: 65, 66, 67}
50: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65}
50: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
50: 68, 69}
50: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67}
50: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67}
50: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
50: 70, 71, 89}
50: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69}
50: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
50: 72, 73, 74, 89, 90, 91}
50: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89}
50: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
50: 75, 76, 77, 89, 90, 91, 92, 93}
50: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
50: 91}
50: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
50: 77, 78, 79, 80, 89, 90, 91}
50: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
50: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
50: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
50: 79, 80, 81, 82, 89}
50: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
50: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
50: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
50: 81, 82, 83, 86}
50: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
50: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
50: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
50: 84, 85, 86, 87, 88}
50: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86}
50: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,
50: 87, 88}
50: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
50: excls[84][num=6]={80, 82, 83, 84, 85, 86}
50: excls[85][num=6]={80, 82, 83, 84, 85, 86}
50: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
50: excls[87][num=6]={80, 82, 83, 86, 87, 88}
50: excls[88][num=6]={80, 82, 83, 86, 87, 88}
50: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
50: 91, 92, 93, 94, 95, 100}
50: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93}
50: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95,
50: 96, 97, 98, 100, 101, 102}
50: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100}
50: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98,
50: 99, 100, 101, 102, 103, 104}
50: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101,
50: 102}
50: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100,
50: 101, 102}
50: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[99][num=6]={93, 95, 96, 97, 98, 99}
50: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101,
50: 102, 103, 104, 105, 106, 115}
50: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104}
50: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105,
50: 106, 107, 108, 109, 115, 116, 117}
50: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115}
50: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107,
50: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
50: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 115, 116, 117}
50: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 110, 111, 112, 113, 114, 115, 116, 117}
50: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 115}
50: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 115}
50: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 113, 114, 115}
50: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114}
50: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114}
50: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 115, 116, 117, 118, 119, 120, 121, 134}
50: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119}
50: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119,
50: 120, 121, 122, 123, 124, 134, 135, 136}
50: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134}
50: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122,
50: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
50: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 134, 135, 136}
50: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136}
50: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 130, 134}
50: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 130, 134}
50: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 127, 128, 129, 130, 131, 132, 133, 134}
50: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 134, 135, 136, 137, 138, 139, 140, 144}
50: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138}
50: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138,
50: 139, 140, 141, 142, 143, 144, 145, 146}
50: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144}
50: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141,
50: 142, 143, 144, 145, 146, 147, 148}
50: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146}
50: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146}
50: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146, 147, 148, 149, 150, 154}
50: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148}
50: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148,
50: 149, 150, 151, 152, 153, 154, 155}
50: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154}
50: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151,
50: 152, 153, 154, 155}
50: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[155][num=6]={146, 148, 149, 150, 154, 155}
50: Bond:
50: nr: 468
50: iatoms:
50: 0 type=100 (BONDS) 0 1
50: 1 type=100 (BONDS) 0 2
50: 2 type=100 (BONDS) 0 3
50: 3 type=101 (BONDS) 0 4
50: 4 type=102 (BONDS) 4 5
50: 5 type=103 (BONDS) 4 6
50: 6 type=104 (BONDS) 4 22
50: 7 type=102 (BONDS) 6 7
50: 8 type=102 (BONDS) 6 8
50: 9 type=103 (BONDS) 6 9
50: 10 type=102 (BONDS) 9 10
50: 11 type=102 (BONDS) 9 11
50: 12 type=103 (BONDS) 9 12
50: 13 type=102 (BONDS) 12 13
50: 14 type=102 (BONDS) 12 14
50: 15 type=103 (BONDS) 12 15
50: 16 type=102 (BONDS) 15 16
50: 17 type=102 (BONDS) 15 17
50: 18 type=101 (BONDS) 15 18
50: 19 type=100 (BONDS) 18 19
50: 20 type=100 (BONDS) 18 20
50: 21 type=100 (BONDS) 18 21
50: 22 type=105 (BONDS) 22 23
50: 23 type=106 (BONDS) 22 24
50: 24 type=100 (BONDS) 24 25
50: 25 type=107 (BONDS) 24 26
50: 26 type=102 (BONDS) 26 27
50: 27 type=103 (BONDS) 26 28
50: 28 type=104 (BONDS) 26 38
50: 29 type=102 (BONDS) 28 29
50: 30 type=103 (BONDS) 28 30
50: 31 type=103 (BONDS) 28 34
50: 32 type=102 (BONDS) 30 31
50: 33 type=102 (BONDS) 30 32
50: 34 type=102 (BONDS) 30 33
50: 35 type=102 (BONDS) 34 35
50: 36 type=102 (BONDS) 34 36
50: 37 type=102 (BONDS) 34 37
50: 38 type=105 (BONDS) 38 39
50: 39 type=106 (BONDS) 38 40
50: 40 type=100 (BONDS) 40 41
50: 41 type=107 (BONDS) 40 42
50: 42 type=102 (BONDS) 42 43
50: 43 type=103 (BONDS) 42 44
50: 44 type=104 (BONDS) 42 58
50: 45 type=102 (BONDS) 44 45
50: 46 type=102 (BONDS) 44 46
50: 47 type=108 (BONDS) 44 47
50: 48 type=109 (BONDS) 47 48
50: 49 type=109 (BONDS) 47 50
50: 50 type=110 (BONDS) 48 49
50: 51 type=109 (BONDS) 48 52
50: 52 type=110 (BONDS) 50 51
50: 53 type=109 (BONDS) 50 54
50: 54 type=110 (BONDS) 52 53
50: 55 type=109 (BONDS) 52 56
50: 56 type=110 (BONDS) 54 55
50: 57 type=109 (BONDS) 54 56
50: 58 type=110 (BONDS) 56 57
50: 59 type=105 (BONDS) 58 59
50: 60 type=106 (BONDS) 58 60
50: 61 type=100 (BONDS) 60 61
50: 62 type=107 (BONDS) 60 62
50: 63 type=102 (BONDS) 62 63
50: 64 type=102 (BONDS) 62 64
50: 65 type=104 (BONDS) 62 65
50: 66 type=105 (BONDS) 65 66
50: 67 type=106 (BONDS) 65 67
50: 68 type=100 (BONDS) 67 68
50: 69 type=107 (BONDS) 67 69
50: 70 type=102 (BONDS) 69 70
50: 71 type=103 (BONDS) 69 71
50: 72 type=104 (BONDS) 69 89
50: 73 type=102 (BONDS) 71 72
50: 74 type=102 (BONDS) 71 73
50: 75 type=103 (BONDS) 71 74
50: 76 type=102 (BONDS) 74 75
50: 77 type=102 (BONDS) 74 76
50: 78 type=103 (BONDS) 74 77
50: 79 type=102 (BONDS) 77 78
50: 80 type=102 (BONDS) 77 79
50: 81 type=111 (BONDS) 77 80
50: 82 type=100 (BONDS) 80 81
50: 83 type=112 (BONDS) 80 82
50: 84 type=112 (BONDS) 82 83
50: 85 type=112 (BONDS) 82 86
50: 86 type=100 (BONDS) 83 84
50: 87 type=100 (BONDS) 83 85
50: 88 type=100 (BONDS) 86 87
50: 89 type=100 (BONDS) 86 88
50: 90 type=105 (BONDS) 89 90
50: 91 type=106 (BONDS) 89 91
50: 92 type=100 (BONDS) 91 92
50: 93 type=107 (BONDS) 91 93
50: 94 type=102 (BONDS) 93 94
50: 95 type=103 (BONDS) 93 95
50: 96 type=104 (BONDS) 93 100
50: 97 type=102 (BONDS) 95 96
50: 98 type=102 (BONDS) 95 97
50: 99 type=113 (BONDS) 95 98
50: 100 type=114 (BONDS) 98 99
50: 101 type=105 (BONDS) 100 101
50: 102 type=106 (BONDS) 100 102
50: 103 type=100 (BONDS) 102 103
50: 104 type=107 (BONDS) 102 104
50: 105 type=102 (BONDS) 104 105
50: 106 type=103 (BONDS) 104 106
50: 107 type=104 (BONDS) 104 115
50: 108 type=102 (BONDS) 106 107
50: 109 type=102 (BONDS) 106 108
50: 110 type=103 (BONDS) 106 109
50: 111 type=102 (BONDS) 109 110
50: 112 type=102 (BONDS) 109 111
50: 113 type=104 (BONDS) 109 112
50: 114 type=115 (BONDS) 112 113
50: 115 type=115 (BONDS) 112 114
50: 116 type=105 (BONDS) 115 116
50: 117 type=106 (BONDS) 115 117
50: 118 type=100 (BONDS) 117 118
50: 119 type=107 (BONDS) 117 119
50: 120 type=102 (BONDS) 119 120
50: 121 type=103 (BONDS) 119 121
50: 122 type=104 (BONDS) 119 134
50: 123 type=102 (BONDS) 121 122
50: 124 type=102 (BONDS) 121 123
50: 125 type=103 (BONDS) 121 124
50: 126 type=102 (BONDS) 124 125
50: 127 type=103 (BONDS) 124 126
50: 128 type=103 (BONDS) 124 130
50: 129 type=102 (BONDS) 126 127
50: 130 type=102 (BONDS) 126 128
50: 131 type=102 (BONDS) 126 129
50: 132 type=102 (BONDS) 130 131
50: 133 type=102 (BONDS) 130 132
50: 134 type=102 (BONDS) 130 133
50: 135 type=105 (BONDS) 134 135
50: 136 type=106 (BONDS) 134 136
50: 137 type=100 (BONDS) 136 137
50: 138 type=107 (BONDS) 136 138
50: 139 type=102 (BONDS) 138 139
50: 140 type=103 (BONDS) 138 140
50: 141 type=104 (BONDS) 138 144
50: 142 type=102 (BONDS) 140 141
50: 143 type=102 (BONDS) 140 142
50: 144 type=102 (BONDS) 140 143
50: 145 type=105 (BONDS) 144 145
50: 146 type=106 (BONDS) 144 146
50: 147 type=100 (BONDS) 146 147
50: 148 type=107 (BONDS) 146 148
50: 149 type=102 (BONDS) 148 149
50: 150 type=103 (BONDS) 148 150
50: 151 type=104 (BONDS) 148 154
50: 152 type=102 (BONDS) 150 151
50: 153 type=102 (BONDS) 150 152
50: 154 type=102 (BONDS) 150 153
50: 155 type=105 (BONDS) 154 155
50: G96Bond:
50: nr: 0
50: Morse:
50: nr: 0
50: Cubic Bonds:
50: nr: 0
50: Connect Bonds:
50: nr: 0
50: Harmonic Pot.:
50: nr: 0
50: FENE Bonds:
50: nr: 0
50: Tab. Bonds:
50: nr: 0
50: Tab. Bonds NC:
50: nr: 0
50: Restraint Pot.:
50: nr: 0
50: Angle:
50: nr: 1124
50: iatoms:
50: 0 type=116 (ANGLES) 1 0 2
50: 1 type=116 (ANGLES) 1 0 3
50: 2 type=116 (ANGLES) 1 0 4
50: 3 type=116 (ANGLES) 2 0 3
50: 4 type=116 (ANGLES) 2 0 4
50: 5 type=116 (ANGLES) 3 0 4
50: 6 type=116 (ANGLES) 0 4 5
50: 7 type=117 (ANGLES) 0 4 6
50: 8 type=117 (ANGLES) 0 4 22
50: 9 type=118 (ANGLES) 5 4 6
50: 10 type=116 (ANGLES) 5 4 22
50: 11 type=119 (ANGLES) 6 4 22
50: 12 type=118 (ANGLES) 4 6 7
50: 13 type=118 (ANGLES) 4 6 8
50: 14 type=120 (ANGLES) 4 6 9
50: 15 type=121 (ANGLES) 7 6 8
50: 16 type=118 (ANGLES) 7 6 9
50: 17 type=118 (ANGLES) 8 6 9
50: 18 type=118 (ANGLES) 6 9 10
50: 19 type=118 (ANGLES) 6 9 11
50: 20 type=120 (ANGLES) 6 9 12
50: 21 type=121 (ANGLES) 10 9 11
50: 22 type=118 (ANGLES) 10 9 12
50: 23 type=118 (ANGLES) 11 9 12
50: 24 type=118 (ANGLES) 9 12 13
50: 25 type=118 (ANGLES) 9 12 14
50: 26 type=120 (ANGLES) 9 12 15
50: 27 type=121 (ANGLES) 13 12 14
50: 28 type=118 (ANGLES) 13 12 15
50: 29 type=118 (ANGLES) 14 12 15
50: 30 type=118 (ANGLES) 12 15 16
50: 31 type=118 (ANGLES) 12 15 17
50: 32 type=117 (ANGLES) 12 15 18
50: 33 type=121 (ANGLES) 16 15 17
50: 34 type=116 (ANGLES) 16 15 18
50: 35 type=116 (ANGLES) 17 15 18
50: 36 type=116 (ANGLES) 15 18 19
50: 37 type=116 (ANGLES) 15 18 20
50: 38 type=116 (ANGLES) 15 18 21
50: 39 type=116 (ANGLES) 19 18 20
50: 40 type=116 (ANGLES) 19 18 21
50: 41 type=116 (ANGLES) 20 18 21
50: 42 type=122 (ANGLES) 4 22 23
50: 43 type=123 (ANGLES) 4 22 24
50: 44 type=124 (ANGLES) 23 22 24
50: 45 type=125 (ANGLES) 22 24 25
50: 46 type=126 (ANGLES) 22 24 26
50: 47 type=127 (ANGLES) 25 24 26
50: 48 type=116 (ANGLES) 24 26 27
50: 49 type=128 (ANGLES) 24 26 28
50: 50 type=129 (ANGLES) 24 26 38
50: 51 type=118 (ANGLES) 27 26 28
50: 52 type=116 (ANGLES) 27 26 38
50: 53 type=119 (ANGLES) 28 26 38
50: 54 type=118 (ANGLES) 26 28 29
50: 55 type=120 (ANGLES) 26 28 30
50: 56 type=120 (ANGLES) 26 28 34
50: 57 type=118 (ANGLES) 29 28 30
50: 58 type=118 (ANGLES) 29 28 34
50: 59 type=120 (ANGLES) 30 28 34
50: 60 type=118 (ANGLES) 28 30 31
50: 61 type=118 (ANGLES) 28 30 32
50: 62 type=118 (ANGLES) 28 30 33
50: 63 type=121 (ANGLES) 31 30 32
50: 64 type=121 (ANGLES) 31 30 33
50: 65 type=121 (ANGLES) 32 30 33
50: 66 type=118 (ANGLES) 28 34 35
50: 67 type=118 (ANGLES) 28 34 36
50: 68 type=118 (ANGLES) 28 34 37
50: 69 type=121 (ANGLES) 35 34 36
50: 70 type=121 (ANGLES) 35 34 37
50: 71 type=121 (ANGLES) 36 34 37
50: 72 type=122 (ANGLES) 26 38 39
50: 73 type=123 (ANGLES) 26 38 40
50: 74 type=124 (ANGLES) 39 38 40
50: 75 type=125 (ANGLES) 38 40 41
50: 76 type=126 (ANGLES) 38 40 42
50: 77 type=127 (ANGLES) 41 40 42
50: 78 type=116 (ANGLES) 40 42 43
50: 79 type=128 (ANGLES) 40 42 44
50: 80 type=129 (ANGLES) 40 42 58
50: 81 type=118 (ANGLES) 43 42 44
50: 82 type=116 (ANGLES) 43 42 58
50: 83 type=119 (ANGLES) 44 42 58
50: 84 type=118 (ANGLES) 42 44 45
50: 85 type=118 (ANGLES) 42 44 46
50: 86 type=130 (ANGLES) 42 44 47
50: 87 type=121 (ANGLES) 45 44 46
50: 88 type=116 (ANGLES) 45 44 47
50: 89 type=116 (ANGLES) 46 44 47
50: 90 type=131 (ANGLES) 44 47 48
50: 91 type=131 (ANGLES) 44 47 50
50: 92 type=132 (ANGLES) 48 47 50
50: 93 type=133 (ANGLES) 47 48 49
50: 94 type=132 (ANGLES) 47 48 52
50: 95 type=133 (ANGLES) 49 48 52
50: 96 type=133 (ANGLES) 47 50 51
50: 97 type=132 (ANGLES) 47 50 54
50: 98 type=133 (ANGLES) 51 50 54
50: 99 type=133 (ANGLES) 48 52 53
50: 100 type=132 (ANGLES) 48 52 56
50: 101 type=133 (ANGLES) 53 52 56
50: 102 type=133 (ANGLES) 50 54 55
50: 103 type=132 (ANGLES) 50 54 56
50: 104 type=133 (ANGLES) 55 54 56
50: 105 type=132 (ANGLES) 52 56 54
50: 106 type=133 (ANGLES) 52 56 57
50: 107 type=133 (ANGLES) 54 56 57
50: 108 type=122 (ANGLES) 42 58 59
50: 109 type=123 (ANGLES) 42 58 60
50: 110 type=124 (ANGLES) 59 58 60
50: 111 type=125 (ANGLES) 58 60 61
50: 112 type=126 (ANGLES) 58 60 62
50: 113 type=127 (ANGLES) 61 60 62
50: 114 type=116 (ANGLES) 60 62 63
50: 115 type=116 (ANGLES) 60 62 64
50: 116 type=129 (ANGLES) 60 62 65
50: 117 type=121 (ANGLES) 63 62 64
50: 118 type=116 (ANGLES) 63 62 65
50: 119 type=116 (ANGLES) 64 62 65
50: 120 type=122 (ANGLES) 62 65 66
50: 121 type=123 (ANGLES) 62 65 67
50: 122 type=124 (ANGLES) 66 65 67
50: 123 type=125 (ANGLES) 65 67 68
50: 124 type=126 (ANGLES) 65 67 69
50: 125 type=127 (ANGLES) 68 67 69
50: 126 type=116 (ANGLES) 67 69 70
50: 127 type=128 (ANGLES) 67 69 71
50: 128 type=129 (ANGLES) 67 69 89
50: 129 type=118 (ANGLES) 70 69 71
50: 130 type=116 (ANGLES) 70 69 89
50: 131 type=119 (ANGLES) 71 69 89
50: 132 type=118 (ANGLES) 69 71 72
50: 133 type=118 (ANGLES) 69 71 73
50: 134 type=120 (ANGLES) 69 71 74
50: 135 type=121 (ANGLES) 72 71 73
50: 136 type=118 (ANGLES) 72 71 74
50: 137 type=118 (ANGLES) 73 71 74
50: 138 type=118 (ANGLES) 71 74 75
50: 139 type=118 (ANGLES) 71 74 76
50: 140 type=120 (ANGLES) 71 74 77
50: 141 type=121 (ANGLES) 75 74 76
50: 142 type=118 (ANGLES) 75 74 77
50: 143 type=118 (ANGLES) 76 74 77
50: 144 type=118 (ANGLES) 74 77 78
50: 145 type=118 (ANGLES) 74 77 79
50: 146 type=117 (ANGLES) 74 77 80
50: 147 type=121 (ANGLES) 78 77 79
50: 148 type=116 (ANGLES) 78 77 80
50: 149 type=116 (ANGLES) 79 77 80
50: 150 type=134 (ANGLES) 77 80 81
50: 151 type=135 (ANGLES) 77 80 82
50: 152 type=133 (ANGLES) 81 80 82
50: 153 type=131 (ANGLES) 80 82 83
50: 154 type=131 (ANGLES) 80 82 86
50: 155 type=131 (ANGLES) 83 82 86
50: 156 type=133 (ANGLES) 82 83 84
50: 157 type=133 (ANGLES) 82 83 85
50: 158 type=133 (ANGLES) 84 83 85
50: 159 type=133 (ANGLES) 82 86 87
50: 160 type=133 (ANGLES) 82 86 88
50: 161 type=133 (ANGLES) 87 86 88
50: 162 type=122 (ANGLES) 69 89 90
50: 163 type=123 (ANGLES) 69 89 91
50: 164 type=124 (ANGLES) 90 89 91
50: 165 type=125 (ANGLES) 89 91 92
50: 166 type=126 (ANGLES) 89 91 93
50: 167 type=127 (ANGLES) 92 91 93
50: 168 type=116 (ANGLES) 91 93 94
50: 169 type=128 (ANGLES) 91 93 95
50: 170 type=129 (ANGLES) 91 93 100
50: 171 type=118 (ANGLES) 94 93 95
50: 172 type=116 (ANGLES) 94 93 100
50: 173 type=119 (ANGLES) 95 93 100
50: 174 type=118 (ANGLES) 93 95 96
50: 175 type=118 (ANGLES) 93 95 97
50: 176 type=136 (ANGLES) 93 95 98
50: 177 type=121 (ANGLES) 96 95 97
50: 178 type=116 (ANGLES) 96 95 98
50: 179 type=116 (ANGLES) 97 95 98
50: 180 type=137 (ANGLES) 95 98 99
50: 181 type=122 (ANGLES) 93 100 101
50: 182 type=123 (ANGLES) 93 100 102
50: 183 type=124 (ANGLES) 101 100 102
50: 184 type=125 (ANGLES) 100 102 103
50: 185 type=126 (ANGLES) 100 102 104
50: 186 type=127 (ANGLES) 103 102 104
50: 187 type=116 (ANGLES) 102 104 105
50: 188 type=128 (ANGLES) 102 104 106
50: 189 type=129 (ANGLES) 102 104 115
50: 190 type=118 (ANGLES) 105 104 106
50: 191 type=116 (ANGLES) 105 104 115
50: 192 type=119 (ANGLES) 106 104 115
50: 193 type=118 (ANGLES) 104 106 107
50: 194 type=118 (ANGLES) 104 106 108
50: 195 type=120 (ANGLES) 104 106 109
50: 196 type=121 (ANGLES) 107 106 108
50: 197 type=118 (ANGLES) 107 106 109
50: 198 type=118 (ANGLES) 108 106 109
50: 199 type=118 (ANGLES) 106 109 110
50: 200 type=118 (ANGLES) 106 109 111
50: 201 type=119 (ANGLES) 106 109 112
50: 202 type=121 (ANGLES) 110 109 111
50: 203 type=116 (ANGLES) 110 109 112
50: 204 type=116 (ANGLES) 111 109 112
50: 205 type=138 (ANGLES) 109 112 113
50: 206 type=138 (ANGLES) 109 112 114
50: 207 type=139 (ANGLES) 113 112 114
50: 208 type=122 (ANGLES) 104 115 116
50: 209 type=123 (ANGLES) 104 115 117
50: 210 type=124 (ANGLES) 116 115 117
50: 211 type=125 (ANGLES) 115 117 118
50: 212 type=126 (ANGLES) 115 117 119
50: 213 type=127 (ANGLES) 118 117 119
50: 214 type=116 (ANGLES) 117 119 120
50: 215 type=128 (ANGLES) 117 119 121
50: 216 type=129 (ANGLES) 117 119 134
50: 217 type=118 (ANGLES) 120 119 121
50: 218 type=116 (ANGLES) 120 119 134
50: 219 type=119 (ANGLES) 121 119 134
50: 220 type=118 (ANGLES) 119 121 122
50: 221 type=118 (ANGLES) 119 121 123
50: 222 type=120 (ANGLES) 119 121 124
50: 223 type=121 (ANGLES) 122 121 123
50: 224 type=118 (ANGLES) 122 121 124
50: 225 type=118 (ANGLES) 123 121 124
50: 226 type=118 (ANGLES) 121 124 125
50: 227 type=120 (ANGLES) 121 124 126
50: 228 type=120 (ANGLES) 121 124 130
50: 229 type=118 (ANGLES) 125 124 126
50: 230 type=118 (ANGLES) 125 124 130
50: 231 type=120 (ANGLES) 126 124 130
50: 232 type=118 (ANGLES) 124 126 127
50: 233 type=118 (ANGLES) 124 126 128
50: 234 type=118 (ANGLES) 124 126 129
50: 235 type=121 (ANGLES) 127 126 128
50: 236 type=121 (ANGLES) 127 126 129
50: 237 type=121 (ANGLES) 128 126 129
50: 238 type=118 (ANGLES) 124 130 131
50: 239 type=118 (ANGLES) 124 130 132
50: 240 type=118 (ANGLES) 124 130 133
50: 241 type=121 (ANGLES) 131 130 132
50: 242 type=121 (ANGLES) 131 130 133
50: 243 type=121 (ANGLES) 132 130 133
50: 244 type=122 (ANGLES) 119 134 135
50: 245 type=123 (ANGLES) 119 134 136
50: 246 type=124 (ANGLES) 135 134 136
50: 247 type=125 (ANGLES) 134 136 137
50: 248 type=126 (ANGLES) 134 136 138
50: 249 type=127 (ANGLES) 137 136 138
50: 250 type=116 (ANGLES) 136 138 139
50: 251 type=128 (ANGLES) 136 138 140
50: 252 type=129 (ANGLES) 136 138 144
50: 253 type=118 (ANGLES) 139 138 140
50: 254 type=116 (ANGLES) 139 138 144
50: 255 type=119 (ANGLES) 140 138 144
50: 256 type=118 (ANGLES) 138 140 141
50: 257 type=118 (ANGLES) 138 140 142
50: 258 type=118 (ANGLES) 138 140 143
50: 259 type=121 (ANGLES) 141 140 142
50: 260 type=121 (ANGLES) 141 140 143
50: 261 type=121 (ANGLES) 142 140 143
50: 262 type=122 (ANGLES) 138 144 145
50: 263 type=123 (ANGLES) 138 144 146
50: 264 type=124 (ANGLES) 145 144 146
50: 265 type=125 (ANGLES) 144 146 147
50: 266 type=126 (ANGLES) 144 146 148
50: 267 type=127 (ANGLES) 147 146 148
50: 268 type=116 (ANGLES) 146 148 149
50: 269 type=128 (ANGLES) 146 148 150
50: 270 type=129 (ANGLES) 146 148 154
50: 271 type=118 (ANGLES) 149 148 150
50: 272 type=116 (ANGLES) 149 148 154
50: 273 type=119 (ANGLES) 150 148 154
50: 274 type=118 (ANGLES) 148 150 151
50: 275 type=118 (ANGLES) 148 150 152
50: 276 type=118 (ANGLES) 148 150 153
50: 277 type=121 (ANGLES) 151 150 152
50: 278 type=121 (ANGLES) 151 150 153
50: 279 type=121 (ANGLES) 152 150 153
50: 280 type=122 (ANGLES) 148 154 155
50: G96Angle:
50: nr: 0
50: Restricted Angles:
50: nr: 0
50: Lin. Angle:
50: nr: 0
50: Bond-Cross:
50: nr: 0
50: BA-Cross:
50: nr: 0
50: U-B:
50: nr: 0
50: Quartic Angles:
50: nr: 0
50: Tab. Angles:
50: nr: 0
50: Proper Dih.:
50: nr: 145
50: iatoms:
50: 0 type=140 (PDIHS) 4 24 22 23
50: 1 type=141 (PDIHS) 22 26 24 25
50: 2 type=140 (PDIHS) 26 40 38 39
50: 3 type=141 (PDIHS) 38 42 40 41
50: 4 type=140 (PDIHS) 42 60 58 59
50: 5 type=142 (PDIHS) 44 47 50 48
50: 6 type=142 (PDIHS) 47 52 48 49
50: 7 type=142 (PDIHS) 47 54 50 51
50: 8 type=142 (PDIHS) 48 56 52 53
50: 9 type=142 (PDIHS) 50 56 54 55
50: 10 type=142 (PDIHS) 52 54 56 57
50: 11 type=141 (PDIHS) 58 62 60 61
50: 12 type=140 (PDIHS) 62 67 65 66
50: 13 type=141 (PDIHS) 65 69 67 68
50: 14 type=140 (PDIHS) 69 91 89 90
50: 15 type=141 (PDIHS) 77 82 80 81
50: 16 type=140 (PDIHS) 80 83 82 86
50: 17 type=141 (PDIHS) 82 84 83 85
50: 18 type=141 (PDIHS) 82 87 86 88
50: 19 type=141 (PDIHS) 89 93 91 92
50: 20 type=140 (PDIHS) 93 102 100 101
50: 21 type=141 (PDIHS) 100 104 102 103
50: 22 type=140 (PDIHS) 104 117 115 116
50: 23 type=140 (PDIHS) 109 113 112 114
50: 24 type=141 (PDIHS) 115 119 117 118
50: 25 type=140 (PDIHS) 119 136 134 135
50: 26 type=141 (PDIHS) 134 138 136 137
50: 27 type=140 (PDIHS) 138 146 144 145
50: 28 type=141 (PDIHS) 144 148 146 147
50: Ryckaert-Bell.:
50: nr: 1565
50: iatoms:
50: 0 type=143 (RBDIHS) 1 0 4 5
50: 1 type=144 (RBDIHS) 1 0 4 6
50: 2 type=144 (RBDIHS) 1 0 4 22
50: 3 type=143 (RBDIHS) 2 0 4 5
50: 4 type=144 (RBDIHS) 2 0 4 6
50: 5 type=144 (RBDIHS) 2 0 4 22
50: 6 type=143 (RBDIHS) 3 0 4 5
50: 7 type=144 (RBDIHS) 3 0 4 6
50: 8 type=144 (RBDIHS) 3 0 4 22
50: 9 type=145 (RBDIHS) 0 4 6 9
50: 10 type=146 (RBDIHS) 22 4 6 9
50: 11 type=147 (RBDIHS) 0 4 6 7
50: 12 type=147 (RBDIHS) 0 4 6 8
50: 13 type=148 (RBDIHS) 5 4 6 7
50: 14 type=148 (RBDIHS) 5 4 6 8
50: 15 type=148 (RBDIHS) 5 4 6 9
50: 16 type=149 (RBDIHS) 22 4 6 7
50: 17 type=149 (RBDIHS) 22 4 6 8
50: 18 type=150 (RBDIHS) 0 4 22 24
50: 19 type=151 (RBDIHS) 6 4 22 24
50: 20 type=148 (RBDIHS) 4 6 9 10
50: 21 type=148 (RBDIHS) 4 6 9 11
50: 22 type=152 (RBDIHS) 4 6 9 12
50: 23 type=148 (RBDIHS) 7 6 9 10
50: 24 type=148 (RBDIHS) 7 6 9 11
50: 25 type=148 (RBDIHS) 7 6 9 12
50: 26 type=148 (RBDIHS) 8 6 9 10
50: 27 type=148 (RBDIHS) 8 6 9 11
50: 28 type=148 (RBDIHS) 8 6 9 12
50: 29 type=148 (RBDIHS) 6 9 12 13
50: 30 type=148 (RBDIHS) 6 9 12 14
50: 31 type=152 (RBDIHS) 6 9 12 15
50: 32 type=148 (RBDIHS) 10 9 12 13
50: 33 type=148 (RBDIHS) 10 9 12 14
50: 34 type=148 (RBDIHS) 10 9 12 15
50: 35 type=148 (RBDIHS) 11 9 12 13
50: 36 type=148 (RBDIHS) 11 9 12 14
50: 37 type=148 (RBDIHS) 11 9 12 15
50: 38 type=148 (RBDIHS) 9 12 15 16
50: 39 type=148 (RBDIHS) 9 12 15 17
50: 40 type=153 (RBDIHS) 9 12 15 18
50: 41 type=148 (RBDIHS) 13 12 15 16
50: 42 type=148 (RBDIHS) 13 12 15 17
50: 43 type=154 (RBDIHS) 13 12 15 18
50: 44 type=148 (RBDIHS) 14 12 15 16
50: 45 type=148 (RBDIHS) 14 12 15 17
50: 46 type=154 (RBDIHS) 14 12 15 18
50: 47 type=144 (RBDIHS) 12 15 18 19
50: 48 type=144 (RBDIHS) 12 15 18 20
50: 49 type=144 (RBDIHS) 12 15 18 21
50: 50 type=143 (RBDIHS) 16 15 18 19
50: 51 type=143 (RBDIHS) 16 15 18 20
50: 52 type=143 (RBDIHS) 16 15 18 21
50: 53 type=143 (RBDIHS) 17 15 18 19
50: 54 type=143 (RBDIHS) 17 15 18 20
50: 55 type=143 (RBDIHS) 17 15 18 21
50: 56 type=155 (RBDIHS) 4 22 24 25
50: 57 type=156 (RBDIHS) 4 22 24 26
50: 58 type=155 (RBDIHS) 23 22 24 25
50: 59 type=157 (RBDIHS) 23 22 24 26
50: 60 type=158 (RBDIHS) 22 24 26 28
50: 61 type=159 (RBDIHS) 22 24 26 38
50: 62 type=160 (RBDIHS) 24 26 28 30
50: 63 type=160 (RBDIHS) 24 26 28 34
50: 64 type=161 (RBDIHS) 38 26 28 30
50: 65 type=161 (RBDIHS) 38 26 28 34
50: 66 type=147 (RBDIHS) 24 26 28 29
50: 67 type=148 (RBDIHS) 27 26 28 29
50: 68 type=148 (RBDIHS) 27 26 28 30
50: 69 type=148 (RBDIHS) 27 26 28 34
50: 70 type=149 (RBDIHS) 38 26 28 29
50: 71 type=150 (RBDIHS) 24 26 38 40
50: 72 type=151 (RBDIHS) 28 26 38 40
50: 73 type=148 (RBDIHS) 26 28 30 31
50: 74 type=148 (RBDIHS) 26 28 30 32
50: 75 type=148 (RBDIHS) 26 28 30 33
50: 76 type=148 (RBDIHS) 29 28 30 31
50: 77 type=148 (RBDIHS) 29 28 30 32
50: 78 type=148 (RBDIHS) 29 28 30 33
50: 79 type=148 (RBDIHS) 34 28 30 31
50: 80 type=148 (RBDIHS) 34 28 30 32
50: 81 type=148 (RBDIHS) 34 28 30 33
50: 82 type=148 (RBDIHS) 26 28 34 35
50: 83 type=148 (RBDIHS) 26 28 34 36
50: 84 type=148 (RBDIHS) 26 28 34 37
50: 85 type=148 (RBDIHS) 29 28 34 35
50: 86 type=148 (RBDIHS) 29 28 34 36
50: 87 type=148 (RBDIHS) 29 28 34 37
50: 88 type=148 (RBDIHS) 30 28 34 35
50: 89 type=148 (RBDIHS) 30 28 34 36
50: 90 type=148 (RBDIHS) 30 28 34 37
50: 91 type=155 (RBDIHS) 26 38 40 41
50: 92 type=156 (RBDIHS) 26 38 40 42
50: 93 type=155 (RBDIHS) 39 38 40 41
50: 94 type=157 (RBDIHS) 39 38 40 42
50: 95 type=158 (RBDIHS) 38 40 42 44
50: 96 type=159 (RBDIHS) 38 40 42 58
50: 97 type=147 (RBDIHS) 40 42 44 45
50: 98 type=147 (RBDIHS) 40 42 44 46
50: 99 type=162 (RBDIHS) 40 42 44 47
50: 100 type=148 (RBDIHS) 43 42 44 45
50: 101 type=148 (RBDIHS) 43 42 44 46
50: 102 type=163 (RBDIHS) 43 42 44 47
50: 103 type=149 (RBDIHS) 58 42 44 45
50: 104 type=149 (RBDIHS) 58 42 44 46
50: 105 type=164 (RBDIHS) 58 42 44 47
50: 106 type=150 (RBDIHS) 40 42 58 60
50: 107 type=151 (RBDIHS) 44 42 58 60
50: 108 type=165 (RBDIHS) 44 47 48 49
50: 109 type=165 (RBDIHS) 44 47 48 52
50: 110 type=165 (RBDIHS) 50 47 48 49
50: 111 type=165 (RBDIHS) 50 47 48 52
50: 112 type=165 (RBDIHS) 44 47 50 51
50: 113 type=165 (RBDIHS) 44 47 50 54
50: 114 type=165 (RBDIHS) 48 47 50 51
50: 115 type=165 (RBDIHS) 48 47 50 54
50: 116 type=165 (RBDIHS) 47 48 52 53
50: 117 type=165 (RBDIHS) 47 48 52 56
50: 118 type=165 (RBDIHS) 49 48 52 53
50: 119 type=165 (RBDIHS) 49 48 52 56
50: 120 type=165 (RBDIHS) 47 50 54 55
50: 121 type=165 (RBDIHS) 47 50 54 56
50: 122 type=165 (RBDIHS) 51 50 54 55
50: 123 type=165 (RBDIHS) 51 50 54 56
50: 124 type=165 (RBDIHS) 48 52 56 54
50: 125 type=165 (RBDIHS) 48 52 56 57
50: 126 type=165 (RBDIHS) 53 52 56 54
50: 127 type=165 (RBDIHS) 53 52 56 57
50: 128 type=165 (RBDIHS) 50 54 56 52
50: 129 type=165 (RBDIHS) 50 54 56 57
50: 130 type=165 (RBDIHS) 55 54 56 52
50: 131 type=165 (RBDIHS) 55 54 56 57
50: 132 type=155 (RBDIHS) 42 58 60 61
50: 133 type=156 (RBDIHS) 42 58 60 62
50: 134 type=155 (RBDIHS) 59 58 60 61
50: 135 type=157 (RBDIHS) 59 58 60 62
50: 136 type=159 (RBDIHS) 58 60 62 65
50: 137 type=150 (RBDIHS) 60 62 65 67
50: 138 type=155 (RBDIHS) 62 65 67 68
50: 139 type=156 (RBDIHS) 62 65 67 69
50: 140 type=155 (RBDIHS) 66 65 67 68
50: 141 type=157 (RBDIHS) 66 65 67 69
50: 142 type=158 (RBDIHS) 65 67 69 71
50: 143 type=159 (RBDIHS) 65 67 69 89
50: 144 type=166 (RBDIHS) 67 69 71 74
50: 145 type=167 (RBDIHS) 89 69 71 74
50: 146 type=147 (RBDIHS) 67 69 71 72
50: 147 type=147 (RBDIHS) 67 69 71 73
50: 148 type=148 (RBDIHS) 70 69 71 72
50: 149 type=148 (RBDIHS) 70 69 71 73
50: 150 type=148 (RBDIHS) 70 69 71 74
50: 151 type=149 (RBDIHS) 89 69 71 72
50: 152 type=149 (RBDIHS) 89 69 71 73
50: 153 type=150 (RBDIHS) 67 69 89 91
50: 154 type=151 (RBDIHS) 71 69 89 91
50: 155 type=148 (RBDIHS) 69 71 74 75
50: 156 type=148 (RBDIHS) 69 71 74 76
50: 157 type=152 (RBDIHS) 69 71 74 77
50: 158 type=148 (RBDIHS) 72 71 74 75
50: 159 type=148 (RBDIHS) 72 71 74 76
50: 160 type=148 (RBDIHS) 72 71 74 77
50: 161 type=148 (RBDIHS) 73 71 74 75
50: 162 type=148 (RBDIHS) 73 71 74 76
50: 163 type=148 (RBDIHS) 73 71 74 77
50: 164 type=148 (RBDIHS) 71 74 77 78
50: 165 type=148 (RBDIHS) 71 74 77 79
50: 166 type=153 (RBDIHS) 71 74 77 80
50: 167 type=148 (RBDIHS) 75 74 77 78
50: 168 type=148 (RBDIHS) 75 74 77 79
50: 169 type=168 (RBDIHS) 75 74 77 80
50: 170 type=148 (RBDIHS) 76 74 77 78
50: 171 type=148 (RBDIHS) 76 74 77 79
50: 172 type=168 (RBDIHS) 76 74 77 80
50: 173 type=169 (RBDIHS) 74 77 80 81
50: 174 type=170 (RBDIHS) 74 77 80 82
50: 175 type=171 (RBDIHS) 78 77 80 82
50: 176 type=171 (RBDIHS) 79 77 80 82
50: 177 type=172 (RBDIHS) 77 80 82 83
50: 178 type=172 (RBDIHS) 77 80 82 86
50: 179 type=173 (RBDIHS) 81 80 82 83
50: 180 type=173 (RBDIHS) 81 80 82 86
50: 181 type=173 (RBDIHS) 80 82 83 84
50: 182 type=173 (RBDIHS) 80 82 83 85
50: 183 type=173 (RBDIHS) 86 82 83 84
50: 184 type=173 (RBDIHS) 86 82 83 85
50: 185 type=173 (RBDIHS) 80 82 86 87
50: 186 type=173 (RBDIHS) 80 82 86 88
50: 187 type=173 (RBDIHS) 83 82 86 87
50: 188 type=173 (RBDIHS) 83 82 86 88
50: 189 type=155 (RBDIHS) 69 89 91 92
50: 190 type=156 (RBDIHS) 69 89 91 93
50: 191 type=155 (RBDIHS) 90 89 91 92
50: 192 type=157 (RBDIHS) 90 89 91 93
50: 193 type=158 (RBDIHS) 89 91 93 95
50: 194 type=159 (RBDIHS) 89 91 93 100
50: 195 type=174 (RBDIHS) 91 93 95 98
50: 196 type=175 (RBDIHS) 100 93 95 98
50: 197 type=147 (RBDIHS) 91 93 95 96
50: 198 type=147 (RBDIHS) 91 93 95 97
50: 199 type=148 (RBDIHS) 94 93 95 96
50: 200 type=148 (RBDIHS) 94 93 95 97
50: 201 type=176 (RBDIHS) 94 93 95 98
50: 202 type=149 (RBDIHS) 100 93 95 96
50: 203 type=149 (RBDIHS) 100 93 95 97
50: 204 type=150 (RBDIHS) 91 93 100 102
50: 205 type=151 (RBDIHS) 95 93 100 102
50: 206 type=177 (RBDIHS) 93 95 98 99
50: 207 type=178 (RBDIHS) 96 95 98 99
50: 208 type=178 (RBDIHS) 97 95 98 99
50: 209 type=155 (RBDIHS) 93 100 102 103
50: 210 type=156 (RBDIHS) 93 100 102 104
50: 211 type=155 (RBDIHS) 101 100 102 103
50: 212 type=157 (RBDIHS) 101 100 102 104
50: 213 type=158 (RBDIHS) 100 102 104 106
50: 214 type=159 (RBDIHS) 100 102 104 115
50: 215 type=179 (RBDIHS) 102 104 106 109
50: 216 type=180 (RBDIHS) 115 104 106 109
50: 217 type=147 (RBDIHS) 102 104 106 107
50: 218 type=147 (RBDIHS) 102 104 106 108
50: 219 type=148 (RBDIHS) 105 104 106 107
50: 220 type=148 (RBDIHS) 105 104 106 108
50: 221 type=148 (RBDIHS) 105 104 106 109
50: 222 type=149 (RBDIHS) 115 104 106 107
50: 223 type=149 (RBDIHS) 115 104 106 108
50: 224 type=150 (RBDIHS) 102 104 115 117
50: 225 type=151 (RBDIHS) 106 104 115 117
50: 226 type=148 (RBDIHS) 104 106 109 110
50: 227 type=148 (RBDIHS) 104 106 109 111
50: 228 type=181 (RBDIHS) 104 106 109 112
50: 229 type=148 (RBDIHS) 107 106 109 110
50: 230 type=148 (RBDIHS) 107 106 109 111
50: 231 type=182 (RBDIHS) 107 106 109 112
50: 232 type=148 (RBDIHS) 108 106 109 110
50: 233 type=148 (RBDIHS) 108 106 109 111
50: 234 type=182 (RBDIHS) 108 106 109 112
50: 235 type=183 (RBDIHS) 106 109 112 113
50: 236 type=183 (RBDIHS) 106 109 112 114
50: 237 type=155 (RBDIHS) 104 115 117 118
50: 238 type=156 (RBDIHS) 104 115 117 119
50: 239 type=155 (RBDIHS) 116 115 117 118
50: 240 type=157 (RBDIHS) 116 115 117 119
50: 241 type=158 (RBDIHS) 115 117 119 121
50: 242 type=159 (RBDIHS) 115 117 119 134
50: 243 type=184 (RBDIHS) 117 119 121 124
50: 244 type=185 (RBDIHS) 134 119 121 124
50: 245 type=147 (RBDIHS) 117 119 121 122
50: 246 type=147 (RBDIHS) 117 119 121 123
50: 247 type=148 (RBDIHS) 120 119 121 122
50: 248 type=148 (RBDIHS) 120 119 121 123
50: 249 type=148 (RBDIHS) 120 119 121 124
50: 250 type=149 (RBDIHS) 134 119 121 122
50: 251 type=149 (RBDIHS) 134 119 121 123
50: 252 type=150 (RBDIHS) 117 119 134 136
50: 253 type=151 (RBDIHS) 121 119 134 136
50: 254 type=148 (RBDIHS) 119 121 124 125
50: 255 type=152 (RBDIHS) 119 121 124 126
50: 256 type=152 (RBDIHS) 119 121 124 130
50: 257 type=148 (RBDIHS) 122 121 124 125
50: 258 type=148 (RBDIHS) 122 121 124 126
50: 259 type=148 (RBDIHS) 122 121 124 130
50: 260 type=148 (RBDIHS) 123 121 124 125
50: 261 type=148 (RBDIHS) 123 121 124 126
50: 262 type=148 (RBDIHS) 123 121 124 130
50: 263 type=148 (RBDIHS) 121 124 126 127
50: 264 type=148 (RBDIHS) 121 124 126 128
50: 265 type=148 (RBDIHS) 121 124 126 129
50: 266 type=148 (RBDIHS) 125 124 126 127
50: 267 type=148 (RBDIHS) 125 124 126 128
50: 268 type=148 (RBDIHS) 125 124 126 129
50: 269 type=148 (RBDIHS) 130 124 126 127
50: 270 type=148 (RBDIHS) 130 124 126 128
50: 271 type=148 (RBDIHS) 130 124 126 129
50: 272 type=148 (RBDIHS) 121 124 130 131
50: 273 type=148 (RBDIHS) 121 124 130 132
50: 274 type=148 (RBDIHS) 121 124 130 133
50: 275 type=148 (RBDIHS) 125 124 130 131
50: 276 type=148 (RBDIHS) 125 124 130 132
50: 277 type=148 (RBDIHS) 125 124 130 133
50: 278 type=148 (RBDIHS) 126 124 130 131
50: 279 type=148 (RBDIHS) 126 124 130 132
50: 280 type=148 (RBDIHS) 126 124 130 133
50: 281 type=155 (RBDIHS) 119 134 136 137
50: 282 type=156 (RBDIHS) 119 134 136 138
50: 283 type=155 (RBDIHS) 135 134 136 137
50: 284 type=157 (RBDIHS) 135 134 136 138
50: 285 type=158 (RBDIHS) 134 136 138 140
50: 286 type=159 (RBDIHS) 134 136 138 144
50: 287 type=147 (RBDIHS) 136 138 140 141
50: 288 type=147 (RBDIHS) 136 138 140 142
50: 289 type=147 (RBDIHS) 136 138 140 143
50: 290 type=148 (RBDIHS) 139 138 140 141
50: 291 type=148 (RBDIHS) 139 138 140 142
50: 292 type=148 (RBDIHS) 139 138 140 143
50: 293 type=149 (RBDIHS) 144 138 140 141
50: 294 type=149 (RBDIHS) 144 138 140 142
50: 295 type=149 (RBDIHS) 144 138 140 143
50: 296 type=150 (RBDIHS) 136 138 144 146
50: 297 type=151 (RBDIHS) 140 138 144 146
50: 298 type=155 (RBDIHS) 138 144 146 147
50: 299 type=156 (RBDIHS) 138 144 146 148
50: 300 type=155 (RBDIHS) 145 144 146 147
50: 301 type=157 (RBDIHS) 145 144 146 148
50: 302 type=158 (RBDIHS) 144 146 148 150
50: 303 type=159 (RBDIHS) 144 146 148 154
50: 304 type=147 (RBDIHS) 146 148 150 151
50: 305 type=147 (RBDIHS) 146 148 150 152
50: 306 type=147 (RBDIHS) 146 148 150 153
50: 307 type=148 (RBDIHS) 149 148 150 151
50: 308 type=148 (RBDIHS) 149 148 150 152
50: 309 type=148 (RBDIHS) 149 148 150 153
50: 310 type=149 (RBDIHS) 154 148 150 151
50: 311 type=149 (RBDIHS) 154 148 150 152
50: 312 type=149 (RBDIHS) 154 148 150 153
50: Restricted Dih.:
50: nr: 0
50: CBT Dih.:
50: nr: 0
50: Fourier Dih.:
50: nr: 0
50: Improper Dih.:
50: nr: 0
50: Improper Dih.:
50: nr: 0
50: Tab. Dih.:
50: nr: 0
50: CMAP Dih.:
50: nr: 0
50: GB 1-2 Pol. (unused):
50: nr: 0
50: GB 1-3 Pol. (unused):
50: nr: 0
50: GB 1-4 Pol. (unused):
50: nr: 0
50: GB Polarization (unused):
50: nr: 0
50: Nonpolar Sol. (unused):
50: nr: 0
50: LJ-14:
50: nr: 1197
50: iatoms:
50: 0 type=186 (LJ14) 0 7
50: 1 type=186 (LJ14) 0 8
50: 2 type=187 (LJ14) 0 9
50: 3 type=188 (LJ14) 0 23
50: 4 type=189 (LJ14) 0 24
50: 5 type=190 (LJ14) 1 5
50: 6 type=190 (LJ14) 1 6
50: 7 type=190 (LJ14) 1 22
50: 8 type=190 (LJ14) 2 5
50: 9 type=190 (LJ14) 2 6
50: 10 type=190 (LJ14) 2 22
50: 11 type=190 (LJ14) 3 5
50: 12 type=190 (LJ14) 3 6
50: 13 type=190 (LJ14) 3 22
50: 14 type=191 (LJ14) 4 10
50: 15 type=191 (LJ14) 4 11
50: 16 type=192 (LJ14) 4 12
50: 17 type=190 (LJ14) 4 25
50: 18 type=192 (LJ14) 4 26
50: 19 type=193 (LJ14) 5 7
50: 20 type=193 (LJ14) 5 8
50: 21 type=191 (LJ14) 5 9
50: 22 type=194 (LJ14) 5 23
50: 23 type=186 (LJ14) 5 24
50: 24 type=191 (LJ14) 6 13
50: 25 type=191 (LJ14) 6 14
50: 26 type=192 (LJ14) 6 15
50: 27 type=195 (LJ14) 6 23
50: 28 type=187 (LJ14) 6 24
50: 29 type=193 (LJ14) 7 10
50: 30 type=193 (LJ14) 7 11
50: 31 type=191 (LJ14) 7 12
50: 32 type=196 (LJ14) 7 22
50: 33 type=193 (LJ14) 8 10
50: 34 type=193 (LJ14) 8 11
50: 35 type=191 (LJ14) 8 12
50: 36 type=196 (LJ14) 8 22
50: 37 type=191 (LJ14) 9 16
50: 38 type=191 (LJ14) 9 17
50: 39 type=187 (LJ14) 9 18
50: 40 type=197 (LJ14) 9 22
50: 41 type=193 (LJ14) 10 13
50: 42 type=193 (LJ14) 10 14
50: 43 type=191 (LJ14) 10 15
50: 44 type=193 (LJ14) 11 13
50: 45 type=193 (LJ14) 11 14
50: 46 type=191 (LJ14) 11 15
50: 47 type=190 (LJ14) 12 19
50: 48 type=190 (LJ14) 12 20
50: 49 type=190 (LJ14) 12 21
50: 50 type=193 (LJ14) 13 16
50: 51 type=193 (LJ14) 13 17
50: 52 type=186 (LJ14) 13 18
50: 53 type=193 (LJ14) 14 16
50: 54 type=193 (LJ14) 14 17
50: 55 type=186 (LJ14) 14 18
50: 56 type=190 (LJ14) 16 19
50: 57 type=190 (LJ14) 16 20
50: 58 type=190 (LJ14) 16 21
50: 59 type=190 (LJ14) 17 19
50: 60 type=190 (LJ14) 17 20
50: 61 type=190 (LJ14) 17 21
50: 62 type=196 (LJ14) 22 27
50: 63 type=197 (LJ14) 22 28
50: 64 type=198 (LJ14) 22 38
50: 65 type=190 (LJ14) 23 25
50: 66 type=195 (LJ14) 23 26
50: 67 type=186 (LJ14) 24 29
50: 68 type=187 (LJ14) 24 30
50: 69 type=187 (LJ14) 24 34
50: 70 type=188 (LJ14) 24 39
50: 71 type=189 (LJ14) 24 40
50: 72 type=190 (LJ14) 25 27
50: 73 type=190 (LJ14) 25 28
50: 74 type=190 (LJ14) 25 38
50: 75 type=191 (LJ14) 26 31
50: 76 type=191 (LJ14) 26 32
50: 77 type=191 (LJ14) 26 33
50: 78 type=191 (LJ14) 26 35
50: 79 type=191 (LJ14) 26 36
50: 80 type=191 (LJ14) 26 37
50: 81 type=190 (LJ14) 26 41
50: 82 type=192 (LJ14) 26 42
50: 83 type=193 (LJ14) 27 29
50: 84 type=191 (LJ14) 27 30
50: 85 type=191 (LJ14) 27 34
50: 86 type=194 (LJ14) 27 39
50: 87 type=186 (LJ14) 27 40
50: 88 type=195 (LJ14) 28 39
50: 89 type=187 (LJ14) 28 40
50: 90 type=193 (LJ14) 29 31
50: 91 type=193 (LJ14) 29 32
50: 92 type=193 (LJ14) 29 33
50: 93 type=193 (LJ14) 29 35
50: 94 type=193 (LJ14) 29 36
50: 95 type=193 (LJ14) 29 37
50: 96 type=196 (LJ14) 29 38
50: 97 type=191 (LJ14) 30 35
50: 98 type=191 (LJ14) 30 36
50: 99 type=191 (LJ14) 30 37
50: 100 type=197 (LJ14) 30 38
50: 101 type=191 (LJ14) 31 34
50: 102 type=191 (LJ14) 32 34
50: 103 type=191 (LJ14) 33 34
50: 104 type=197 (LJ14) 34 38
50: 105 type=196 (LJ14) 38 43
50: 106 type=197 (LJ14) 38 44
50: 107 type=198 (LJ14) 38 58
50: 108 type=190 (LJ14) 39 41
50: 109 type=195 (LJ14) 39 42
50: 110 type=186 (LJ14) 40 45
50: 111 type=186 (LJ14) 40 46
50: 112 type=199 (LJ14) 40 47
50: 113 type=188 (LJ14) 40 59
50: 114 type=189 (LJ14) 40 60
50: 115 type=190 (LJ14) 41 43
50: 116 type=190 (LJ14) 41 44
50: 117 type=190 (LJ14) 41 58
50: 118 type=200 (LJ14) 42 48
50: 119 type=200 (LJ14) 42 50
50: 120 type=190 (LJ14) 42 61
50: 121 type=192 (LJ14) 42 62
50: 122 type=193 (LJ14) 43 45
50: 123 type=193 (LJ14) 43 46
50: 124 type=201 (LJ14) 43 47
50: 125 type=194 (LJ14) 43 59
50: 126 type=186 (LJ14) 43 60
50: 127 type=202 (LJ14) 44 49
50: 128 type=202 (LJ14) 44 51
50: 129 type=200 (LJ14) 44 52
50: 130 type=200 (LJ14) 44 54
50: 131 type=195 (LJ14) 44 59
50: 132 type=187 (LJ14) 44 60
50: 133 type=201 (LJ14) 45 48
50: 134 type=201 (LJ14) 45 50
50: 135 type=196 (LJ14) 45 58
50: 136 type=201 (LJ14) 46 48
50: 137 type=201 (LJ14) 46 50
50: 138 type=196 (LJ14) 46 58
50: 139 type=203 (LJ14) 47 53
50: 140 type=203 (LJ14) 47 55
50: 141 type=204 (LJ14) 47 56
50: 142 type=205 (LJ14) 47 58
50: 143 type=203 (LJ14) 48 51
50: 144 type=204 (LJ14) 48 54
50: 145 type=203 (LJ14) 48 57
50: 146 type=203 (LJ14) 49 50
50: 147 type=206 (LJ14) 49 53
50: 148 type=203 (LJ14) 49 56
50: 149 type=204 (LJ14) 50 52
50: 150 type=203 (LJ14) 50 57
50: 151 type=206 (LJ14) 51 55
50: 152 type=203 (LJ14) 51 56
50: 153 type=203 (LJ14) 52 55
50: 154 type=203 (LJ14) 53 54
50: 155 type=206 (LJ14) 53 57
50: 156 type=206 (LJ14) 55 57
50: 157 type=196 (LJ14) 58 63
50: 158 type=196 (LJ14) 58 64
50: 159 type=198 (LJ14) 58 65
50: 160 type=190 (LJ14) 59 61
50: 161 type=195 (LJ14) 59 62
50: 162 type=188 (LJ14) 60 66
50: 163 type=189 (LJ14) 60 67
50: 164 type=190 (LJ14) 61 63
50: 165 type=190 (LJ14) 61 64
50: 166 type=190 (LJ14) 61 65
50: 167 type=190 (LJ14) 62 68
50: 168 type=192 (LJ14) 62 69
50: 169 type=194 (LJ14) 63 66
50: 170 type=186 (LJ14) 63 67
50: 171 type=194 (LJ14) 64 66
50: 172 type=186 (LJ14) 64 67
50: 173 type=196 (LJ14) 65 70
50: 174 type=197 (LJ14) 65 71
50: 175 type=198 (LJ14) 65 89
50: 176 type=190 (LJ14) 66 68
50: 177 type=195 (LJ14) 66 69
50: 178 type=186 (LJ14) 67 72
50: 179 type=186 (LJ14) 67 73
50: 180 type=187 (LJ14) 67 74
50: 181 type=188 (LJ14) 67 90
50: 182 type=189 (LJ14) 67 91
50: 183 type=190 (LJ14) 68 70
50: 184 type=190 (LJ14) 68 71
50: 185 type=190 (LJ14) 68 89
50: 186 type=191 (LJ14) 69 75
50: 187 type=191 (LJ14) 69 76
50: 188 type=192 (LJ14) 69 77
50: 189 type=190 (LJ14) 69 92
50: 190 type=192 (LJ14) 69 93
50: 191 type=193 (LJ14) 70 72
50: 192 type=193 (LJ14) 70 73
50: 193 type=191 (LJ14) 70 74
50: 194 type=194 (LJ14) 70 90
50: 195 type=186 (LJ14) 70 91
50: 196 type=191 (LJ14) 71 78
50: 197 type=191 (LJ14) 71 79
50: 198 type=187 (LJ14) 71 80
50: 199 type=195 (LJ14) 71 90
50: 200 type=187 (LJ14) 71 91
50: 201 type=193 (LJ14) 72 75
50: 202 type=193 (LJ14) 72 76
50: 203 type=191 (LJ14) 72 77
50: 204 type=196 (LJ14) 72 89
50: 205 type=193 (LJ14) 73 75
50: 206 type=193 (LJ14) 73 76
50: 207 type=191 (LJ14) 73 77
50: 208 type=196 (LJ14) 73 89
50: 209 type=190 (LJ14) 74 81
50: 210 type=207 (LJ14) 74 82
50: 211 type=197 (LJ14) 74 89
50: 212 type=193 (LJ14) 75 78
50: 213 type=193 (LJ14) 75 79
50: 214 type=186 (LJ14) 75 80
50: 215 type=193 (LJ14) 76 78
50: 216 type=193 (LJ14) 76 79
50: 217 type=186 (LJ14) 76 80
50: 218 type=187 (LJ14) 77 83
50: 219 type=187 (LJ14) 77 86
50: 220 type=190 (LJ14) 78 81
50: 221 type=208 (LJ14) 78 82
50: 222 type=190 (LJ14) 79 81
50: 223 type=208 (LJ14) 79 82
50: 224 type=190 (LJ14) 80 84
50: 225 type=190 (LJ14) 80 85
50: 226 type=190 (LJ14) 80 87
50: 227 type=190 (LJ14) 80 88
50: 228 type=190 (LJ14) 81 83
50: 229 type=190 (LJ14) 81 86
50: 230 type=190 (LJ14) 83 87
50: 231 type=190 (LJ14) 83 88
50: 232 type=190 (LJ14) 84 86
50: 233 type=190 (LJ14) 85 86
50: 234 type=196 (LJ14) 89 94
50: 235 type=197 (LJ14) 89 95
50: 236 type=198 (LJ14) 89 100
50: 237 type=190 (LJ14) 90 92
50: 238 type=195 (LJ14) 90 93
50: 239 type=186 (LJ14) 91 96
50: 240 type=186 (LJ14) 91 97
50: 241 type=209 (LJ14) 91 98
50: 242 type=188 (LJ14) 91 101
50: 243 type=189 (LJ14) 91 102
50: 244 type=190 (LJ14) 92 94
50: 245 type=190 (LJ14) 92 95
50: 246 type=190 (LJ14) 92 100
50: 247 type=190 (LJ14) 93 99
50: 248 type=190 (LJ14) 93 103
50: 249 type=192 (LJ14) 93 104
50: 250 type=193 (LJ14) 94 96
50: 251 type=193 (LJ14) 94 97
50: 252 type=210 (LJ14) 94 98
50: 253 type=194 (LJ14) 94 101
50: 254 type=186 (LJ14) 94 102
50: 255 type=195 (LJ14) 95 101
50: 256 type=187 (LJ14) 95 102
50: 257 type=190 (LJ14) 96 99
50: 258 type=196 (LJ14) 96 100
50: 259 type=190 (LJ14) 97 99
50: 260 type=196 (LJ14) 97 100
50: 261 type=211 (LJ14) 98 100
50: 262 type=196 (LJ14) 100 105
50: 263 type=197 (LJ14) 100 106
50: 264 type=198 (LJ14) 100 115
50: 265 type=190 (LJ14) 101 103
50: 266 type=195 (LJ14) 101 104
50: 267 type=186 (LJ14) 102 107
50: 268 type=186 (LJ14) 102 108
50: 269 type=187 (LJ14) 102 109
50: 270 type=188 (LJ14) 102 116
50: 271 type=189 (LJ14) 102 117
50: 272 type=190 (LJ14) 103 105
50: 273 type=190 (LJ14) 103 106
50: 274 type=190 (LJ14) 103 115
50: 275 type=191 (LJ14) 104 110
50: 276 type=191 (LJ14) 104 111
50: 277 type=197 (LJ14) 104 112
50: 278 type=190 (LJ14) 104 118
50: 279 type=192 (LJ14) 104 119
50: 280 type=193 (LJ14) 105 107
50: 281 type=193 (LJ14) 105 108
50: 282 type=191 (LJ14) 105 109
50: 283 type=194 (LJ14) 105 116
50: 284 type=186 (LJ14) 105 117
50: 285 type=195 (LJ14) 106 113
50: 286 type=195 (LJ14) 106 114
50: 287 type=195 (LJ14) 106 116
50: 288 type=187 (LJ14) 106 117
50: 289 type=193 (LJ14) 107 110
50: 290 type=193 (LJ14) 107 111
50: 291 type=196 (LJ14) 107 112
50: 292 type=196 (LJ14) 107 115
50: 293 type=193 (LJ14) 108 110
50: 294 type=193 (LJ14) 108 111
50: 295 type=196 (LJ14) 108 112
50: 296 type=196 (LJ14) 108 115
50: 297 type=197 (LJ14) 109 115
50: 298 type=194 (LJ14) 110 113
50: 299 type=194 (LJ14) 110 114
50: 300 type=194 (LJ14) 111 113
50: 301 type=194 (LJ14) 111 114
50: 302 type=196 (LJ14) 115 120
50: 303 type=197 (LJ14) 115 121
50: 304 type=198 (LJ14) 115 134
50: 305 type=190 (LJ14) 116 118
50: 306 type=195 (LJ14) 116 119
50: 307 type=186 (LJ14) 117 122
50: 308 type=186 (LJ14) 117 123
50: 309 type=187 (LJ14) 117 124
50: 310 type=188 (LJ14) 117 135
50: 311 type=189 (LJ14) 117 136
50: 312 type=190 (LJ14) 118 120
50: 313 type=190 (LJ14) 118 121
50: 314 type=190 (LJ14) 118 134
50: 315 type=191 (LJ14) 119 125
50: 316 type=192 (LJ14) 119 126
50: 317 type=192 (LJ14) 119 130
50: 318 type=190 (LJ14) 119 137
50: 319 type=192 (LJ14) 119 138
50: 320 type=193 (LJ14) 120 122
50: 321 type=193 (LJ14) 120 123
50: 322 type=191 (LJ14) 120 124
50: 323 type=194 (LJ14) 120 135
50: 324 type=186 (LJ14) 120 136
50: 325 type=191 (LJ14) 121 127
50: 326 type=191 (LJ14) 121 128
50: 327 type=191 (LJ14) 121 129
50: 328 type=191 (LJ14) 121 131
50: 329 type=191 (LJ14) 121 132
50: 330 type=191 (LJ14) 121 133
50: 331 type=195 (LJ14) 121 135
50: 332 type=187 (LJ14) 121 136
50: 333 type=193 (LJ14) 122 125
50: 334 type=191 (LJ14) 122 126
50: 335 type=191 (LJ14) 122 130
50: 336 type=196 (LJ14) 122 134
50: 337 type=193 (LJ14) 123 125
50: 338 type=191 (LJ14) 123 126
50: 339 type=191 (LJ14) 123 130
50: 340 type=196 (LJ14) 123 134
50: 341 type=197 (LJ14) 124 134
50: 342 type=193 (LJ14) 125 127
50: 343 type=193 (LJ14) 125 128
50: 344 type=193 (LJ14) 125 129
50: 345 type=193 (LJ14) 125 131
50: 346 type=193 (LJ14) 125 132
50: 347 type=193 (LJ14) 125 133
50: 348 type=191 (LJ14) 126 131
50: 349 type=191 (LJ14) 126 132
50: 350 type=191 (LJ14) 126 133
50: 351 type=191 (LJ14) 127 130
50: 352 type=191 (LJ14) 128 130
50: 353 type=191 (LJ14) 129 130
50: 354 type=196 (LJ14) 134 139
50: 355 type=197 (LJ14) 134 140
50: 356 type=198 (LJ14) 134 144
50: 357 type=190 (LJ14) 135 137
50: 358 type=195 (LJ14) 135 138
50: 359 type=186 (LJ14) 136 141
50: 360 type=186 (LJ14) 136 142
50: 361 type=186 (LJ14) 136 143
50: 362 type=188 (LJ14) 136 145
50: 363 type=189 (LJ14) 136 146
50: 364 type=190 (LJ14) 137 139
50: 365 type=190 (LJ14) 137 140
50: 366 type=190 (LJ14) 137 144
50: 367 type=190 (LJ14) 138 147
50: 368 type=192 (LJ14) 138 148
50: 369 type=193 (LJ14) 139 141
50: 370 type=193 (LJ14) 139 142
50: 371 type=193 (LJ14) 139 143
50: 372 type=194 (LJ14) 139 145
50: 373 type=186 (LJ14) 139 146
50: 374 type=195 (LJ14) 140 145
50: 375 type=187 (LJ14) 140 146
50: 376 type=196 (LJ14) 141 144
50: 377 type=196 (LJ14) 142 144
50: 378 type=196 (LJ14) 143 144
50: 379 type=196 (LJ14) 144 149
50: 380 type=197 (LJ14) 144 150
50: 381 type=198 (LJ14) 144 154
50: 382 type=190 (LJ14) 145 147
50: 383 type=195 (LJ14) 145 148
50: 384 type=186 (LJ14) 146 151
50: 385 type=186 (LJ14) 146 152
50: 386 type=186 (LJ14) 146 153
50: 387 type=188 (LJ14) 146 155
50: 388 type=190 (LJ14) 147 149
50: 389 type=190 (LJ14) 147 150
50: 390 type=190 (LJ14) 147 154
50: 391 type=193 (LJ14) 149 151
50: 392 type=193 (LJ14) 149 152
50: 393 type=193 (LJ14) 149 153
50: 394 type=194 (LJ14) 149 155
50: 395 type=195 (LJ14) 150 155
50: 396 type=196 (LJ14) 151 154
50: 397 type=196 (LJ14) 152 154
50: 398 type=196 (LJ14) 153 154
50: Coulomb-14:
50: nr: 0
50: LJC-14 q:
50: nr: 0
50: LJC Pairs NB:
50: nr: 0
50: LJ (SR):
50: nr: 0
50: Buck.ham (SR):
50: nr: 0
50: LJ (unused):
50: nr: 0
50: B.ham (unused):
50: nr: 0
50: Disper. corr.:
50: nr: 0
50: Coulomb (SR):
50: nr: 0
50: Coul (unused):
50: nr: 0
50: RF excl.:
50: nr: 0
50: Coul. recip.:
50: nr: 0
50: LJ recip.:
50: nr: 0
50: DPD:
50: nr: 0
50: Polarization:
50: nr: 0
50: Water Pol.:
50: nr: 0
50: Thole Pol.:
50: nr: 0
50: Anharm. Pol.:
50: nr: 0
50: Position Rest.:
50: nr: 0
50: Flat-bottom posres:
50: nr: 0
50: Dis. Rest.:
50: nr: 0
50: D.R.Viol. (nm):
50: nr: 0
50: Orient. Rest.:
50: nr: 0
50: Ori. R. RMSD:
50: nr: 0
50: Angle Rest.:
50: nr: 0
50: Angle Rest. Z:
50: nr: 0
50: Dih. Rest.:
50: nr: 0
50: Dih. Rest. Viol.:
50: nr: 0
50: Constraint:
50: nr: 0
50: Constr. No Conn.:
50: nr: 0
50: Settle:
50: nr: 0
50: Virtual site 1:
50: nr: 0
50: Virtual site 2:
50: nr: 0
50: Virtual site 2fd:
50: nr: 0
50: Virtual site 3:
50: nr: 0
50: Virtual site 3fd:
50: nr: 0
50: Virtual site 3fad:
50: nr: 0
50: Virtual site 3out:
50: nr: 0
50: Virtual site 4fd:
50: nr: 0
50: Virtual site 4fdn:
50: nr: 0
50: Virtual site N:
50: nr: 0
50: COM Pull En.:
50: nr: 0
50: Density fitting:
50: nr: 0
50: Quantum En.:
50: nr: 0
50: Potential:
50: nr: 0
50: Kinetic En.:
50: nr: 0
50: Total Energy:
50: nr: 0
50: Conserved En.:
50: nr: 0
50: Temperature:
50: nr: 0
50: Vir. Temp. (not used):
50: nr: 0
50: Pres. DC:
50: nr: 0
50: Pressure:
50: nr: 0
50: dH/dl constr.:
50: nr: 0
50: dVremain/dl:
50: nr: 0
50: dEkin/dl:
50: nr: 0
50: dVcoul/dl:
50: nr: 0
50: dVvdw/dl:
50: nr: 0
50: dVbonded/dl:
50: nr: 0
50: dVrestraint/dl:
50: nr: 0
50: dVtemperature/dl:
50: nr: 0
50: grp[T-Coupling ] nr=1, name=[ rest]
50: grp[Energy Mon. ] nr=1, name=[ rest]
50: grp[Acceleration] nr=1, name=[ rest]
50: grp[Freeze ] nr=1, name=[ rest]
50: grp[User1 ] nr=1, name=[ rest]
50: grp[User2 ] nr=1, name=[ rest]
50: grp[VCM ] nr=1, name=[ rest]
50: grp[Compressed X] nr=1, name=[ rest]
50: grp[Or. Res. Fit] nr=1, name=[ rest]
50: grp[QMMM ] nr=1, name=[ rest]
50: grpname (11):
50: grpname[0]={name="System"}
50: grpname[1]={name="Protein"}
50: grpname[2]={name="Protein-H"}
50: grpname[3]={name="C-alpha"}
50: grpname[4]={name="Backbone"}
50: grpname[5]={name="MainChain"}
50: grpname[6]={name="MainChain+Cb"}
50: grpname[7]={name="MainChain+H"}
50: grpname[8]={name="SideChain"}
50: grpname[9]={name="SideChain-H"}
50: grpname[10]={name="rest"}
50: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
50: allocated 0 0 0 0 0 0 0 0 0 0
50: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
50: box (3x3):
50: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
50: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
50: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
50: box_rel (3x3):
50: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv (3x3):
50: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev (3x3):
50: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev (3x3):
50: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev (3x3):
50: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: nosehoover_xi: not available
50: x (156x3):
50: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
50: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
50: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
50: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
50: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
50: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
50: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
50: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
50: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
50: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
50: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
50: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
50: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
50: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
50: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
50: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
50: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
50: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
50: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
50: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
50: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
50: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
50: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
50: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
50: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
50: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
50: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
50: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
50: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
50: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
50: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
50: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
50: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
50: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
50: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
50: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
50: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
50: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
50: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
50: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
50: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
50: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
50: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
50: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
50: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
50: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
50: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
50: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
50: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
50: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
50: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
50: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
50: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
50: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
50: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
50: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
50: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
50: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
50: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
50: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
50: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
50: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
50: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
50: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
50: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
50: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
50: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
50: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
50: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
50: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
50: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
50: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
50: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
50: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
50: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
50: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
50: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
50: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
50: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
50: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
50: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
50: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
50: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
50: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
50: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
50: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
50: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
50: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
50: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
50: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
50: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
50: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
50: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
50: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
50: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
50: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
50: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
50: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
50: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
50: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
50: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
50: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
50: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
50: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
50: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
50: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
50: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
50: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
50: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
50: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
50: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
50: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
50: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
50: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
50: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
50: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
50: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
50: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
50: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
50: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
50: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
50: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
50: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
50: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
50: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
50: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
50: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
50: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
50: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
50: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
50: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
50: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
50: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
50: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
50: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
50: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
50: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
50: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
50: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
50: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
50: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
50: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
50: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
50: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
50: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
50: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
50: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
50: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
50: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
50: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
50: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
50: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
50: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
50: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
50: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
50: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
50: v (156x3):
50: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: Group statistics
50: T-Coupling : 156 (total 156 atoms)
50: Energy Mon. : 156 (total 156 atoms)
50: Acceleration: 156 (total 156 atoms)
50: Freeze : 156 (total 156 atoms)
50: User1 : 156 (total 156 atoms)
50: User2 : 156 (total 156 atoms)
50: VCM : 156 (total 156 atoms)
50: Compressed X: 156 (total 156 atoms)
50: Or. Res. Fit: 156 (total 156 atoms)
50: QMMM : 156 (total 156 atoms)
50: [ OK ] DumpTest.WorksWithTpr (29 ms)
50: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
50: [ OK ] DumpTest.WorksWithTprAndMdpWriting (3 ms)
50: [----------] 2 tests from DumpTest (32 ms total)
50:
50: [----------] 3 tests from HelpwritingTest
50: [ RUN ] HelpwritingTest.ConvertTprWritesHelp
50: [ OK ] HelpwritingTest.ConvertTprWritesHelp (1 ms)
50: [ RUN ] HelpwritingTest.DumpWritesHelp
50: [ OK ] HelpwritingTest.DumpWritesHelp (6 ms)
50: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp
50: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (1 ms)
50: [----------] 3 tests from HelpwritingTest (8 ms total)
50:
50: [----------] 4 tests from ReportMethodsTest
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: For a correct single-point energy evaluation with nsteps = 0, use
50: continuation = yes to avoid constraining the input coordinates.
50:
50: Generating 1-4 interactions: fudge = 0.5
50:
50: NOTE 2 [file lysozyme.top, line 1465]:
50: System has non-zero total charge: 2.000000
50: Total charge should normally be an integer. See
50: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
50: for discussion on how close it should be to an integer.
50:
50:
50:
50: Number of degrees of freedom in T-Coupling group rest is 465.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: NVE simulation with an initial temperature of zero: will use a Verlet
50: buffer of 10%. Check your energy drift!
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Setting the LD random seed to 2078948713
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50:
50: Generated 330891 of the 330891 1-4 parameter combinations
50:
50: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
50: Analysing residue names:
50: There are: 10 Protein residues
50: Analysing Protein...
50:
50: This run will generate roughly 0 Mb of data
50: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
50: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
50: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
50: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
50: [ RUN ] ReportMethodsTest.WritesCorrectInformation
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
50: [ OK ] ReportMethodsTest.WritesCorrectInformation (2 ms)
50: [ RUN ] ReportMethodsTest.ToolEndToEndTest
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
50: section: Methods
50: subsection: Simulation system
50: A system of 1 molecules (156 atoms) was simulated.
50:
50: subsection: Simulation settings
50: A total of 0 ns were simulated with a time step of 1 fs.
50: Neighbor searching was performed every 10 steps.
50: The Cut-off algorithm was used for electrostatic interactions.
50: with a cut-off of 1 nm.
50: A single cut-off of 1.1 nm was used for Van der Waals interactions.
50: [ OK ] ReportMethodsTest.ToolEndToEndTest (2 ms)
50: [----------] 4 tests from ReportMethodsTest (4 ms total)
50:
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: trr version: GMX_trn_file (single precision)
50:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (7 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (8 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (7 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from gro file '', 6 atoms.
50:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (7 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
50: -> frame 0 time 0.000
't= 0.00000', 6 atoms
50:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (7 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (7 ms)
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (43 ms total)
50:
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (3 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from gro file '', 6 atoms.
50:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
50: -> frame 0 time 0.000
't= 0.00000', 6 atoms
50:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (2 ms)
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (13 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 21 tests from 5 test cases ran. (4395 ms total)
50: [ PASSED ] 21 tests.
50/65 Test #50: ToolUnitTests ......................... Passed 4.44 sec
test 51
Start 51: FileIOTests
51: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FileIOTests.xml"
51: Test timeout computed to be: 30
51: [==========] Running 42 tests from 10 test cases.
51: [----------] Global test environment set-up.
51: [----------] 4 tests from Checkpoint
51: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent
51: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms)
51: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent
51: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms)
51: [ RUN ] Checkpoint.KvtRoundTripInt64
51: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms)
51: [ RUN ] Checkpoint.KvtRoundTripReal
51: [ OK ] Checkpoint.KvtRoundTripReal (0 ms)
51: [----------] 4 tests from Checkpoint (1 ms total)
51:
51: [----------] 2 tests from FileMD5Test
51: [ RUN ] FileMD5Test.CanComputeMD5
51: [ OK ] FileMD5Test.CanComputeMD5 (3 ms)
51: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
51: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms)
51: [----------] 2 tests from FileMD5Test (4 ms total)
51:
51: [----------] 3 tests from MrcSerializer
51: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
51: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
51: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
51: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (1 ms)
51: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
51: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (2 ms)
51: [----------] 3 tests from MrcSerializer (3 ms total)
51:
51: [----------] 4 tests from MrcDensityMap
51: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
51: [ OK ] MrcDensityMap.RoundTripIsIdempotent (2 ms)
51: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
51: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (1 ms)
51: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
51: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms)
51: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
51: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (7 ms)
51: [----------] 4 tests from MrcDensityMap (11 ms total)
51:
51: [----------] 8 tests from MrcDensityMapHeaderTest
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
51: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
51: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
51: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.IsSane
51: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
51: [----------] 8 tests from MrcDensityMapHeaderTest (1 ms total)
51:
51: [----------] 10 tests from ReadTest
51: [ RUN ] ReadTest.get_eint_ReadsInteger
51: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side '0.8' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
51: [ RUN ] ReadTest.get_eint_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.get_eint64_ReadsInteger
51: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side '0.8' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
51: [ RUN ] ReadTest.get_eint64_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.get_ereal_ReadsInteger
51: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_ereal_ReadsFloat
51: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
51: [ RUN ] ReadTest.get_ereal_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not a
51: real value
51:
51:
51: [ OK ] ReadTest.get_ereal_WarnsAboutString (1 ms)
51: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString
51: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms)
51: [----------] 10 tests from ReadTest (2 ms total)
51:
51: [----------] 1 test from FileIOXdrSerializerTest
51: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
51: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms)
51: [----------] 1 test from FileIOXdrSerializerTest (1 ms total)
51:
51: [----------] 2 tests from TngTest
51: [ RUN ] TngTest.CanOpenTngFile
51: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
51: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
51: [ OK ] TngTest.CanOpenTngFile (0 ms)
51: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
51: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
51: [----------] 2 tests from TngTest (1 ms total)
51:
51: [----------] 4 tests from XvgioTest
51: [ RUN ] XvgioTest.readXvgIntWorks
51: [ OK ] XvgioTest.readXvgIntWorks (0 ms)
51: [ RUN ] XvgioTest.readXvgRealWorks
51: [ OK ] XvgioTest.readXvgRealWorks (0 ms)
51: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks
51: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (1 ms)
51: [ RUN ] XvgioTest.readXvgDeprecatedWorks
51: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms)
51: [----------] 4 tests from XvgioTest (2 ms total)
51:
51: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (2 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (4 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (2 ms)
51: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (9 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 42 tests from 10 test cases ran. (38 ms total)
51: [ PASSED ] 42 tests.
51/65 Test #51: FileIOTests ........................... Passed 0.07 sec
test 52
Start 52: SelectionUnitTests
52: Test command: /<<PKGBUILDDIR>>/build/basic/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SelectionUnitTests.xml"
52: Test timeout computed to be: 30
52: [==========] Running 192 tests from 11 test cases.
52: [----------] Global test environment set-up.
52: [----------] 1 test from IndexGroupTest
52: [ RUN ] IndexGroupTest.RemovesDuplicates
52: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
52: [----------] 1 test from IndexGroupTest (0 ms total)
52:
52: [----------] 15 tests from IndexBlockTest
52: [ RUN ] IndexBlockTest.CreatesUnknownBlock
52: [ OK ] IndexBlockTest.CreatesUnknownBlock (43 ms)
52: [ RUN ] IndexBlockTest.CreatesAtomBlock
52: [ OK ] IndexBlockTest.CreatesAtomBlock (1 ms)
52: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
52: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (7 ms)
52: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
52: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (7 ms)
52: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
52: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms)
52: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
52: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (1 ms)
52: [ RUN ] IndexBlockTest.CreatesSingleBlock
52: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
52: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (8 ms)
52: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
52: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
52: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (1 ms)
52: [----------] 15 tests from IndexBlockTest (70 ms total)
52:
52: [----------] 11 tests from IndexMapTest
52: [ RUN ] IndexMapTest.InitializesAtomBlock
52: [ OK ] IndexMapTest.InitializesAtomBlock (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
52: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
52: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
52: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
52: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
52: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (1 ms)
52: [ RUN ] IndexMapTest.InitializesMoleculeBlock
52: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms)
52: [ RUN ] IndexMapTest.MapsSingleBlock
52: [ OK ] IndexMapTest.MapsSingleBlock (1 ms)
52: [ RUN ] IndexMapTest.MapsResidueBlocks
52: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms)
52: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
52: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (1 ms)
52: [ RUN ] IndexMapTest.HandlesMultipleRequests
52: [ OK ] IndexMapTest.HandlesMultipleRequests (13 ms)
52: [----------] 11 tests from IndexMapTest (22 ms total)
52:
52: [----------] 3 tests from IndexGroupsAndNamesTest
52: [ RUN ] IndexGroupsAndNamesTest.containsNames
52: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
52: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
52: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms)
52: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
52: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (1 ms)
52: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total)
52:
52: [----------] 15 tests from NeighborhoodSearchTest
52: [ RUN ] NeighborhoodSearchTest.SimpleSearch
52: [ OK ] NeighborhoodSearchTest.SimpleSearch (48 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
52: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (48 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchBox
52: [ OK ] NeighborhoodSearchTest.GridSearchBox (6 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
52: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (23 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
52: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (13 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
52: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (4 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
52: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (6 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
52: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (1 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
52: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (96 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
52: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
52: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
52: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
52: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
52: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (9 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
52: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (2 ms)
52: [----------] 15 tests from NeighborhoodSearchTest (258 ms total)
52:
52: [----------] 12 tests from PositionCalculationTest
52: [ RUN ] PositionCalculationTest.ComputesAtomPositions
52: [ OK ] PositionCalculationTest.ComputesAtomPositions (73 ms)
52: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
52: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (66 ms)
52: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
52: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
52: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
52: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
52: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
52: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionMask
52: [ OK ] PositionCalculationTest.ComputesPositionMask (1 ms)
52: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
52: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms)
52: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
52: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms)
52: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
52: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (1 ms)
52: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
52: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms)
52: [----------] 12 tests from PositionCalculationTest (150 ms total)
52:
52: [----------] 29 tests from SelectionCollectionTest
52: [ RUN ] SelectionCollectionTest.HandlesNoSelections
52: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
52: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (33 ms)
52: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
52: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
52: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms)
52: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
52: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
52: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
52: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
52: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
52: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
52: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
52: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
52: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (2 ms)
52: [----------] 29 tests from SelectionCollectionTest (60 ms total)
52:
52: [----------] 14 tests from SelectionCollectionInteractiveTest
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
52: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
52: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
52: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
52: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
52: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
52: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms)
52: [----------] 14 tests from SelectionCollectionInteractiveTest (19 ms total)
52:
52: [----------] 66 tests from SelectionCollectionDataTest
52: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
52: [ OK ] SelectionCollectionDataTest.HandlesAllNone (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
52: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResnr
52: [ OK ] SelectionCollectionDataTest.HandlesResnr (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
52: [ OK ] SelectionCollectionDataTest.HandlesResIndex (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
52: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
52: [ OK ] SelectionCollectionDataTest.HandlesAtomname (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
52: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
52: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesChain
52: [ OK ] SelectionCollectionDataTest.HandlesChain (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMass
52: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesCharge
52: [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
52: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
52: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
52: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBeta
52: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResname
52: [ OK ] SelectionCollectionDataTest.HandlesResname (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
52: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
52: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (8 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (12 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
52: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (6 ms)
52: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
52: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (4 ms)
52: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
52: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
52: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
52: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (10 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
52: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
52: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
52: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
52: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
52: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
52: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
52: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
52: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
52: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
52: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
52: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
52: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
52: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (6 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
52: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
52: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
52: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
52: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
52: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
52: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
52: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
52: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
52: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
52: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
52: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (2 ms)
52: [----------] 66 tests from SelectionCollectionDataTest (187 ms total)
52:
52: [----------] 17 tests from SelectionOptionTest
52: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
52: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
52: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
52: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (1 ms)
52: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
52: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (1 ms)
52: [ RUN ] SelectionOptionTest.ChecksEmptySelections
52: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
52: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
52: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooManySelections
52: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
52: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
52: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesAdjuster
52: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
52: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
52: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
52: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms)
52: [----------] 17 tests from SelectionOptionTest (13 ms total)
52:
52: [----------] 9 tests from SelectionFileOptionTest
52: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
52: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
52: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
52: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
52: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
52: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
52: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
52: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
52: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
52: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms)
52: [----------] 9 tests from SelectionFileOptionTest (7 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 192 tests from 11 test cases ran. (788 ms total)
52: [ PASSED ] 192 tests.
52/65 Test #52: SelectionUnitTests .................... Passed 0.83 sec
test 53
Start 53: MdrunOutputTests
53: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunOutputTests.xml"
53: Test timeout computed to be: 600
53: [==========] Running 12 tests from 5 test cases.
53: [----------] Global test environment set-up.
53: [----------] 1 test from MdrunTest
53: [ RUN ] MdrunTest.WritesHelp
53: No protocol specified
53: [ OK ] MdrunTest.WritesHelp (41 ms)
53: [----------] 1 test from MdrunTest (41 ms total)
53:
53: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
53: No protocol specified
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -421265409
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.328 0.164 199.8
53: (ns/day) (hour/ns)
53: Performance: 1.053 22.793
53:
Reading frame 0 time 0.000
53: # Atoms 6
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (193 ms)
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to 1709162431
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.333 0.167 199.8
53: (ns/day) (hour/ns)
53: Performance: 1.036 23.157
53:
Reading frame 0 time 0.000
53: # Atoms 6
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (190 ms)
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to 2002809191
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.368 0.184 199.8
53: (ns/day) (hour/ns)
53: Performance: 0.940 25.543
53:
Reading frame 0 time 0.000
53: # Atoms 3
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (208 ms)
53: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (592 ms total)
53:
53: [----------] 2 tests from Argon12/OutputFiles
53: No protocol specified
53: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
53: that with the Verlet scheme, nstlist has no effect on the accuracy of
53: your simulation.
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: Setting nstcalcenergy (100) equal to nstenergy (4)
53:
53: Number of degrees of freedom in T-Coupling group System is 33.00
53:
53: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: NVE simulation: will use the initial temperature of 68.810 K for
53: determining the Verlet buffer size
53:
53:
53: There were 3 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'Argon'
53: 16 steps, 0.0 ps.
53: Generated 1 of the 1 non-bonded parameter combinations
53:
53: Excluding 1 bonded neighbours molecule type 'Argon'
53:
53: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
53:
53: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.357 0.178 199.8
53: (ns/day) (hour/ns)
53: Performance: 8.230 2.916
53: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (200 ms)
53: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
53: that with the Verlet scheme, nstlist has no effect on the accuracy of
53: your simulation.
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: Setting nstcalcenergy (100) equal to nstenergy (4)
53:
53: Number of degrees of freedom in T-Coupling group System is 33.00
53:
53: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: NVE simulation: will use the initial temperature of 68.810 K for
53: determining the Verlet buffer size
53:
53:
53: There were 3 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'Argon'
53: 16 steps, 0.0 ps.
53: Generated 1 of the 1 non-bonded parameter combinations
53:
53: Excluding 1 bonded neighbours molecule type 'Argon'
53:
53: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
53:
53: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.339 0.169 199.9
53: (ns/day) (hour/ns)
53: Performance: 8.669 2.769
53: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (191 ms)
53: [----------] 2 tests from Argon12/OutputFiles (392 ms total)
53:
53: [----------] 3 tests from MdrunCanWrite/Trajectories
53: No protocol specified
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to -1216479745
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.424 0.212 199.8
53: (ns/day) (hour/ns)
53: Performance: 2.851 8.417
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (236 ms)
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to 1757375903
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.271 0.135 199.7
53: (ns/day) (hour/ns)
53: Performance: 4.465 5.375
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (157 ms)
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to -26116379
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.268 0.134 199.7
53: (ns/day) (hour/ns)
53: Performance: 4.513 5.317
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (158 ms)
53: [----------] 3 tests from MdrunCanWrite/Trajectories (552 ms total)
53:
53: [----------] 3 tests from MdrunCanWrite/NptTrajectories
53: No protocol specified
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to -8569987
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.309 0.154 199.8
53: (ns/day) (hour/ns)
53: Performance: 1.678 14.300
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (177 ms)
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to 2063531900
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.270 0.135 199.7
53: (ns/day) (hour/ns)
53: Performance: 1.919 12.508
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (158 ms)
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to -562090049
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.253 0.127 199.7
53: (ns/day) (hour/ns)
53: Performance: 2.043 11.745
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (150 ms)
53: [----------] 3 tests from MdrunCanWrite/NptTrajectories (486 ms total)
53:
53: [----------] Global test environment tear-down
53: [==========] 12 tests from 5 test cases ran. (2155 ms total)
53: [ PASSED ] 12 tests.
53/65 Test #53: MdrunOutputTests ...................... Passed 2.19 sec
test 54
Start 54: MdrunModulesTests
54: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunModulesTests.xml"
54: Test timeout computed to be: 600
54: [==========] Running 15 tests from 3 test cases.
54: [----------] Global test environment set-up.
54: [----------] 9 tests from DensityFittingTest
54: No protocol specified
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -3.8565400e+03
54: Maximum force = 2.8846870e+03 on atom 3
54: Norm of force = 1.0754448e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -34115585
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (33 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -9.8208447e+03
54: Maximum force = 4.7331094e+03 on atom 2
54: Norm of force = 1.7801224e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -1212252169
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (20 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (17 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -9.7604385e+03
54: Maximum force = 4.6344800e+03 on atom 2
54: Norm of force = 1.7575605e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to 1136523263
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (21 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (16 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -3.8565400e+03
54: Maximum force = 2.8846870e+03 on atom 3
54: Norm of force = 1.0754448e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -277345427
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (20 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -2.7138666e+04
54: Maximum force = 4.3409717e+03 on atom 2
54: Norm of force = 1.2549793e+03
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -314843669
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (20 ms)
54: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: Setting the LD random seed to -139481089
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (19 ms)
54: [ RUN ] DensityFittingTest.CheckpointWorks
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
54: Setting nstcalcenergy (100) equal to nstenergy (2)
54:
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
54: NVE simulation: will use the initial temperature of 68.810 K for
54: determining the Verlet buffer size
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting mdrun 'Argon'
54: 2 steps, 0.0 ps.
54: Setting the LD random seed to 2128079547
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.250 0.125 199.8
54: (ns/day) (hour/ns)
54: Performance: 2.072 11.585
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
54: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
54: Can not increase nstlist because an NVE ensemble is used
54:
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting mdrun 'Argon'
54: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.297 0.149 199.8
54: (ns/day) (hour/ns)
54: Performance: 2.903 8.269
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (306 ms)
54: [----------] 9 tests from DensityFittingTest (473 ms total)
54:
54: [----------] 4 tests from MimicTest
54: No protocol specified
54: [ RUN ] MimicTest.OneQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.002 0.001 189.9
54: (ns/day) (hour/ns)
54: Performance: 67.965 0.353
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -74057859
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.OneQuantumMol (19 ms)
54: [ RUN ] MimicTest.AllQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.002 0.001 189.8
54: (ns/day) (hour/ns)
54: Performance: 70.027 0.343
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1377846433
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.AllQuantumMol (23 ms)
54: [ RUN ] MimicTest.TwoQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.002 0.001 189.6
54: (ns/day) (hour/ns)
54: Performance: 70.054 0.343
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -220334083
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.TwoQuantumMol (22 ms)
54: [ RUN ] MimicTest.BondCuts
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 66.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: NVE simulation: will use the initial temperature of 300.368 K for
54: determining the Verlet buffer size
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
54:
54: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.003 0.002 192.4
54: (ns/day) (hour/ns)
54: Performance: 54.193 0.443
54: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 2098806650
54:
54: Generated 2211 of the 2211 non-bonded parameter combinations
54:
54: Generated 2211 of the 2211 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.BondCuts (96 ms)
54: [----------] 4 tests from MimicTest (164 ms total)
54:
54: [----------] 2 tests from WithIntegrator/ImdTest
54: No protocol specified
54: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
54: Generating 1-4 interactions: fudge = 1
54:
54: NOTE 1 [file glycine_vacuo.top, line 12]:
54: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
54: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
54: Number of degrees of freedom in T-Coupling group System is 27.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
54: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
54:
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: IMD: Enabled. This simulation will accept incoming IMD connections.
54: IMD: Pulling from IMD remote is enabled (-imdpull).
54: IMD: Setting port for connection requests to 0.
54: IMD: Setting up incoming socket.
54: IMD: Listening for IMD connection on port 57059.
54: IMD: -imdwait not set, starting simulation.
54: starting mdrun 'Glycine'
54: 2 steps, 0.0 ps.
54: Setting the LD random seed to -537395905
54:
54: Generated 20503 of the 20503 non-bonded parameter combinations
54:
54: Generated 17396 of the 20503 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Glycine'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.363 0.182 199.8
54: (ns/day) (hour/ns)
54: Performance: 2.855 8.407
54: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (622 ms)
54: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
54: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
54: apply to steep.
54:
54: Generating 1-4 interactions: fudge = 1
54: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
54: Number of degrees of freedom in T-Coupling group System is 27.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: IMD: Enabled. This simulation will accept incoming IMD connections.
54: IMD: Pulling from IMD remote is enabled (-imdpull).
54: IMD: Setting port for connection requests to 0.
54: IMD: Setting up incoming socket.
54: IMD: Listening for IMD connection on port 47117.
54: IMD: -imdwait not set, starting simulation.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = 1.1977063e+03
54: Maximum force = 1.7794877e+04 on atom 9
54: Norm of force = 7.8732901e+03
54: Setting the LD random seed to 254635989
54:
54: Generated 20503 of the 20503 non-bonded parameter combinations
54:
54: Generated 17396 of the 20503 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Glycine'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (418 ms)
54: [----------] 2 tests from WithIntegrator/ImdTest (1041 ms total)
54:
54: [----------] Global test environment tear-down
54: [==========] 15 tests from 3 test cases ran. (1745 ms total)
54: [ PASSED ] 15 tests.
54/65 Test #54: MdrunModulesTests ..................... Passed 1.78 sec
test 55
Start 55: MdrunIOTests
55: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunIOTests.xml"
55: Test timeout computed to be: 600
55: [==========] Running 61 tests from 10 test cases.
55: [----------] Global test environment set-up.
55: [----------] 3 tests from GromppTest
55: No protocol specified
55: [ RUN ] GromppTest.EmptyMdpFileWorks
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Number of degrees of freedom in T-Coupling group rest is 12.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to 1588968379
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.EmptyMdpFileWorks (13 ms)
55: [ RUN ] GromppTest.SimulatedAnnealingWorks
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Simulated annealing for group rest: Periodic, 4 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 2.0 320.0
55: 4.0 320.0
55: 6.0 298.0
55: Number of degrees of freedom in T-Coupling group rest is 12.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -1075953926
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.SimulatedAnnealingWorks (12 ms)
55: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Simulated annealing for group Methanol: Single, 3 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 3.0 280.0
55: 6.0- 270.0
55: Simulated annealing for group SOL: Periodic, 4 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 2.0 320.0
55: 4.0 320.0
55: 6.0 298.0
55: Number of degrees of freedom in T-Coupling group Methanol is 7.20
55: Number of degrees of freedom in T-Coupling group SOL is 4.80
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -169623553
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (12 ms)
55: [----------] 3 tests from GromppTest (37 ms total)
55:
55: [----------] 6 tests from MdrunTerminationTest
55: No protocol specified
55: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -286287105
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.378 0.189 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.372 17.498
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.275 0.138 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.880 12.763
55: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (358 ms)
55: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 1, rlist from 1.024 to 1
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 100 steps, 0.1 ps.
55:
55: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
55: Setting the LD random seed to 1843345359
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.281 0.141 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.844 13.019
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Setting nsteps to 102
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 100
55: Runtime for the run 0.1 ps
55: Run end step 100
55: Run end time 0.1 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 102
55: Runtime for the run 0.102 ps
55: Run end step 102
55: Run end time 0.102 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.326 0.163 199.8
55: (ns/day) (hour/ns)
55: Performance: 53.526 0.448
55: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (332 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -136332961
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.264 0.132 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.959 12.253
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.283 0.142 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.828 13.130
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Setting nsteps to 6
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 6
55: Runtime for the run 0.006 ps
55: Run end step 6
55: Run end time 0.006 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.497 0.249 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.043 23.009
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Setting nsteps to 8
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 6
55: Runtime for the run 0.006 ps
55: Run end step 6
55: Run end time 0.006 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 8
55: Runtime for the run 0.008 ps
55: Run end step 8
55: Run end time 0.008 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.334 0.167 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.552 15.467
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.002 0.001 185.0
55: (ns/day) (hour/ns)
55: Performance: 77.682 0.309
55: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (740 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -813084741
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.263 0.132 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.967 12.203
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps.
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.285 0.143 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.031 7.918
55: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (299 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -536936513
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.297 0.149 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.745 13.752
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Setting nsteps to 4
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (167 ms)
55: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to 1978843103
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.310 0.155 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.669 14.377
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.400 0.200 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.294 18.546
55: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (380 ms)
55: [----------] 6 tests from MdrunTerminationTest (2277 ms total)
55:
55: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks
55: No protocol specified
55: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.405 0.203 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.251 3.310
55: trr version: GMX_trn_file (single precision)
55:
55:
55: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (221 ms)
55: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.314 0.157 199.9
55: (ns/day) (hour/ns)
55: Performance: 9.352 2.566
55:
55:
55: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (174 ms)
55: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (395 ms total)
55:
55: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
55: No protocol specified
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.418 0.209 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.027 3.415
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.322 0.161 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.820 4.979
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.519 0.260 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.992 8.021
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (670 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.375 0.188 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.829 3.066
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.339 0.170 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.584 5.235
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.402 0.201 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.866 6.208
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (597 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.324 0.162 199.8
55: (ns/day) (hour/ns)
55: Performance: 9.064 2.648
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.306 0.153 199.7
55: (ns/day) (hour/ns)
55: Performance: 5.083 4.722
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.536 0.268 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.900 8.275
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (616 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.375 0.188 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.833 3.064
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.289 0.145 199.7
55: (ns/day) (hour/ns)
55: Performance: 5.379 4.462
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.319 0.159 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.879 4.919
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (530 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.390 0.195 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.530 3.187
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.358 0.179 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.336 5.535
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.586 0.293 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.654 9.042
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (699 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.390 0.195 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.528 3.188
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.355 0.178 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.374 5.488
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.336 0.168 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.626 5.188
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (582 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.371 0.185 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.919 3.031
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.341 0.171 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.556 5.268
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.300 0.150 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.184 4.630
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (548 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.323 0.162 199.9
55: (ns/day) (hour/ns)
55: Performance: 9.087 2.641
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.501 0.251 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.102 7.736
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.336 0.168 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.626 5.188
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (630 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.404 0.202 199.8
55: (ns/day) (hour/ns)
55: Performance: 7.265 3.303
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.387 0.194 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.016 5.977
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.438 0.219 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.546 6.769
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (749 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.471 0.236 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.227 3.854
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.390 0.195 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.987 6.019
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.438 0.219 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.552 6.757
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (754 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.382 0.191 199.8
55: (ns/day) (hour/ns)
55: Performance: 7.680 3.125
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.611 0.306 199.8
55: (ns/day) (hour/ns)
55: Performance: 2.541 9.444
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.410 0.205 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.790 6.333
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (840 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.389 0.195 199.8
55: (ns/day) (hour/ns)
55: Performance: 7.537 3.184
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.326 0.163 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.765 5.037
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.171 0.586 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.327 18.082
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (1073 ms)
55: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (8289 ms total)
55:
55: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
55: No protocol specified
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.493 0.247 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.949 4.035
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.528 0.264 199.8
55: (ns/day) (hour/ns)
55: Performance: 2.941 8.160
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.798 0.399 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.947 12.327
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1041 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.515 0.257 199.9
55: (ns/day) (hour/ns)
55: Performance: 5.706 4.206
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.452 0.226 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.440 6.977
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.698 0.349 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.227 10.777
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (925 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.377 0.189 199.8
55: (ns/day) (hour/ns)
55: Performance: 7.792 3.080
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.469 0.235 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.314 7.243
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.420 0.210 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.702 6.484
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (813 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.709 0.355 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.141 5.795
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.449 0.225 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.455 6.946
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.428 0.214 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.631 6.609
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (911 ms)
55: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (3691 ms total)
55:
55: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
55: No protocol specified
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 1.854 0.927 200.0
55: (ns/day) (hour/ns)
55: Performance: 1.584 15.147
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.403 0.202 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.858 6.221
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.333 0.167 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.667 5.142
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1339 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.567 0.284 199.9
55: (ns/day) (hour/ns)
55: Performance: 5.176 4.637
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.336 0.168 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.624 5.191
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.388 0.194 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.008 5.988
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (689 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.384 0.192 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.648 3.138
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.305 0.153 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.098 4.708
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.627 0.313 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.481 9.672
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (704 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.374 0.187 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.848 3.058
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.324 0.162 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.793 5.007
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.369 0.185 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.214 5.695
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (565 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.359 0.179 199.9
55: (ns/day) (hour/ns)
55: Performance: 8.189 2.931
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.521 0.261 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.984 8.044
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.369 0.185 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.208 5.703
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (657 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.410 0.205 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.159 3.352
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.388 0.194 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.007 5.989
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.373 0.187 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.164 5.763
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (622 ms)
55: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (4577 ms total)
55:
55: [----------] 6 tests from NPH/MdrunNoAppendContinuationIsExact
55: No protocol specified
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.577 0.288 199.9
55: (ns/day) (hour/ns)
55: Performance: 5.092 4.713
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.375 0.187 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.148 5.786
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.357 0.179 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.356 5.510
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (683 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.425 0.212 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.914 3.471
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.374 0.187 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.150 5.783
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.623 0.311 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.497 9.611
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (739 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.374 0.187 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.848 3.058
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.325 0.162 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.787 5.014
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.340 0.170 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.570 5.251
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (548 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.408 0.204 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.197 3.335
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.308 0.154 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.049 4.754
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.473 0.237 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.286 7.303
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (623 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.425 0.212 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.913 3.472
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.408 0.204 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.812 6.297
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.389 0.195 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.992 6.011
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (639 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.324 0.162 199.9
55: (ns/day) (hour/ns)
55: Performance: 9.063 2.648
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.374 0.187 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.151 5.782
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.539 0.270 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.883 8.325
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (648 ms)
55: [----------] 6 tests from NPH/MdrunNoAppendContinuationIsExact (3881 ms total)
55:
55: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact
55: No protocol specified
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.328 0.164 199.9
55: (ns/day) (hour/ns)
55: Performance: 8.955 2.680
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.324 0.162 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.788 5.013
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.473 0.236 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.288 7.299
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (592 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.374 0.187 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.843 3.060
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.590 0.295 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.634 9.113
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.484 0.242 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.211 7.475
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (756 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.391 0.195 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.513 3.194
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.358 0.179 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.344 5.525
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.323 0.162 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.806 4.994
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (564 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.424 0.212 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.921 3.468
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.358 0.179 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.343 5.526
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.323 0.162 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.810 4.990
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (581 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.541 0.270 199.9
55: (ns/day) (hour/ns)
55: Performance: 5.431 4.419
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.358 0.179 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.345 5.524
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.324 0.162 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.798 5.002
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (641 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.377 0.189 199.8
55: (ns/day) (hour/ns)
55: Performance: 7.786 3.083
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.371 0.186 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.189 5.729
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.340 0.170 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.573 5.248
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (580 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55:
55: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Using Berendsen pressure coupling invalidates the true ensemble for the
55: thermostat
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: There was 1 warning
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55:
55: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Using Berendsen pressure coupling invalidates the true ensemble for the
55: thermostat
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: There was 1 warning
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.341 0.171 199.9
55: (ns/day) (hour/ns)
55: Performance: 8.606 2.789
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.358 0.179 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.337 5.534
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.536 0.268 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.901 8.273
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (648 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.378 0.189 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.776 3.087
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.308 0.154 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.049 4.754
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.373 0.187 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.163 5.765
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (565 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.407 0.204 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.207 3.330
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.491 0.245 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.168 7.575
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.390 0.195 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.989 6.017
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (673 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.408 0.204 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.203 3.332
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.308 0.154 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.048 4.754
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.423 0.212 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.674 6.533
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (598 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.574 0.287 199.9
55: (ns/day) (hour/ns)
55: Performance: 5.115 4.692
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.374 0.187 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.160 5.769
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.454 0.227 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.425 7.008
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (731 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.372 0.186 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.882 3.045
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.323 0.162 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.807 4.993
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.555 0.278 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.802 8.565
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (655 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.373 0.187 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.868 3.050
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.357 0.178 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.357 5.508
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.405 0.203 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.836 6.257
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (599 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.407 0.204 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.208 3.330
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.637 0.319 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.440 9.836
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.443 0.222 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.508 6.842
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (781 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.323 0.162 199.9
55: (ns/day) (hour/ns)
55: Performance: 9.080 2.643
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.308 0.154 199.7
55: (ns/day) (hour/ns)
55: Performance: 5.049 4.753
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.504 0.252 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.085 7.779
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (599 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15
55: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (0 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16
55: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (0 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.589 0.295 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.984 4.815
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.305 0.153 199.7
55: (ns/day) (hour/ns)
55: Performance: 5.097 4.708
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.340 0.170 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.573 5.248
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (655 ms)
55: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (10220 ms total)
55:
55: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
55: No protocol specified
55: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.411 0.205 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.148 3.358
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.375 0.188 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.145 5.790
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.582 0.291 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.669 8.992
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (717 ms)
55: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (717 ms total)
55:
55: [----------] 3 tests from Checking/InitialConstraintsTest
55: No protocol specified
55: [ RUN ] Checking/InitialConstraintsTest.Works/0
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to -5259853
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.354 0.177 199.9
55: (ns/day) (hour/ns)
55: Performance: 0.977 24.573
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (191 ms)
55: [ RUN ] Checking/InitialConstraintsTest.Works/1
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to 1610086253
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.288 0.144 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.198 20.028
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (158 ms)
55: [ RUN ] Checking/InitialConstraintsTest.Works/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: Integrator method md-vv-avek is implemented primarily for validation
55: purposes; for molecular dynamics, you should probably be using md or md-vv
55:
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to -402667009
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.304 0.152 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.136 21.126
55: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (166 ms)
55: [----------] 3 tests from Checking/InitialConstraintsTest (515 ms total)
55:
55: [----------] Global test environment tear-down
55: [==========] 61 tests from 10 test cases ran. (34782 ms total)
55: [ PASSED ] 61 tests.
55/65 Test #55: MdrunIOTests .......................... Passed 34.82 sec
test 56
Start 56: MdrunTests
56: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTests.xml"
56: Test timeout computed to be: 600
56: [==========] Running 14 tests from 6 test cases.
56: [----------] Global test environment set-up.
56: [----------] 1 test from OriresTest
56: No protocol specified
56: [ RUN ] OriresTest.OriresCanRun
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
56: The Berendsen thermostat does not generate the correct kinetic energy
56: distribution. You might want to consider using the V-rescale thermostat.
56:
56: Generating 1-4 interactions: fudge = 0.5
56: Number of degrees of freedom in T-Coupling group System is 518.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
56: You are using a plain Coulomb cut-off, which might produce artifacts.
56: You might want to consider using PME electrostatics.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
56: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
56:
56:
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
56: 10 steps, 0.0 ps.
56: Setting the LD random seed to -1765814275
56:
56: Generated 2145 of the 2145 non-bonded parameter combinations
56:
56: Generated 2145 of the 2145 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
56:
56: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
56:
56: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
56:
56: Note that mdrun will redetermine rlist based on the actual pair-list setup
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.430 0.215 199.9
56: (ns/day) (hour/ns)
56: Performance: 8.827 2.719
56: [ OK ] OriresTest.OriresCanRun (628 ms)
56: [----------] 1 test from OriresTest (629 ms total)
56:
56: [----------] 1 test from CompelTest
56: No protocol specified
56: [ RUN ] CompelTest.SwapCanRun
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: The Berendsen thermostat does not generate the correct kinetic energy
56: distribution. You might want to consider using the V-rescale thermostat.
56:
56: Generating 1-4 interactions: fudge = 0.5
56: Split0 group 'Ch0' contains 83 atoms.
56: Split1 group 'Ch1' contains 83 atoms.
56: Solvent group 'SOL' contains 11931 atoms.
56: Swap group 'NA+' contains 19 atoms.
56: Swap group 'CL-' contains 19 atoms.
56: Number of degrees of freedom in T-Coupling group System is 27869.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: You are using a plain Coulomb cut-off, which might produce artifacts.
56: You might want to consider using PME electrostatics.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: SWAP: Determining initial numbers of ions per compartment.
56: SWAP: Setting pointers for checkpoint writing
56: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
56: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
56: starting mdrun 'Channel_coco in octane membrane'
56: 2 steps, 0.0 ps.
56: Setting the LD random seed to -1073759233
56:
56: Generated 330891 of the 330891 non-bonded parameter combinations
56:
56: Generated 330891 of the 330891 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein'
56:
56: turning all bonds into constraints...
56:
56: Excluding 3 bonded neighbours molecule type 'OCT'
56:
56: turning all bonds into constraints...
56:
56: Excluding 1 bonded neighbours molecule type 'NA'
56:
56: turning all bonds into constraints...
56:
56: Excluding 1 bonded neighbours molecule type 'CL'
56:
56: turning all bonds into constraints...
56:
56: Excluding 3 bonded neighbours molecule type 'Protein'
56:
56: Excluding 3 bonded neighbours molecule type 'OCT'
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning all bonds into constraints...
56:
56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
56:
56: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
56:
56: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
56:
56: Note that mdrun will redetermine rlist based on the actual pair-list setup
56:
56: This run will generate roughly 1 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 2.280 1.140 200.0
56: (ns/day) (hour/ns)
56: Performance: 1.137 21.113
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
56:
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: SWAP: Setting pointers for checkpoint writing
56: SWAP: Copying channel fluxes from checkpoint file data
56: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
56: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
56: starting mdrun 'Channel_coco in octane membrane'
56: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 2.158 1.079 200.0
56: (ns/day) (hour/ns)
56: Performance: 1.201 19.986
56: [ OK ] CompelTest.SwapCanRun (4372 ms)
56: [----------] 1 test from CompelTest (4372 ms total)
56:
56: [----------] 6 tests from BondedInteractionsTest
56: No protocol specified
56: [ RUN ] BondedInteractionsTest.NormalBondWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 2 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.001 0.001 184.0
56: (ns/day) (hour/ns)
56: Performance: 132.597 0.181
56: Setting the LD random seed to 739901437
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalBondWorks (16 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 2 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.001 0.001 184.5
56: (ns/day) (hour/ns)
56: Performance: 134.069 0.179
56: Setting the LD random seed to -83984677
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedBondWorks (19 ms)
56: [ RUN ] BondedInteractionsTest.NormalAngleWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.001 0.001 183.9
56: (ns/day) (hour/ns)
56: Performance: 131.110 0.183
56: Setting the LD random seed to -373303065
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalAngleWorks (17 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.001 0.001 184.2
56: (ns/day) (hour/ns)
56: Performance: 131.730 0.182
56: Setting the LD random seed to -101620231
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (18 ms)
56: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.001 0.001 184.5
56: (ns/day) (hour/ns)
56: Performance: 130.168 0.184
56: Setting the LD random seed to -134237513
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalDihedralWorks (15 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.001 0.001 183.7
56: (ns/day) (hour/ns)
56: Performance: 131.969 0.182
56: Setting the LD random seed to 1887366911
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (21 ms)
56: [----------] 6 tests from BondedInteractionsTest (107 ms total)
56:
56: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest
56: No protocol specified
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0
56: Number of degrees of freedom in T-Coupling group rest is 10.00
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'Dipoles'
56: 20 steps, 0.1 ps.
56: Setting the LD random seed to -1075348225
56:
56: Generated 1 of the 1 non-bonded parameter combinations
56:
56: Excluding 1 bonded neighbours molecule type 'Dipole'
56:
56: Searching the wall atom type(s)
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200
56:
56: Estimate for the relative computational load of the PME mesh part: 1.00
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.481 0.241 199.8
56: (ns/day) (hour/ns)
56: Performance: 18.848 1.273
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision)
56:
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (39581 ms)
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1
56: Test system 'epsilon-surface-constraint' cannot run with 1 ranks.
56: The supported numbers are > 1.
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms)
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: With epsilon_surface > 0 all molecules should be neutral.
56:
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: With epsilon_surface > 0 you can only use domain decomposition when there
56: are only small molecules with all bonds constrained (mdrun will check for
56: this).
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 4 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'Dipoles'
56: 20 steps, 0.1 ps.
56: Setting the LD random seed to -1107305483
56:
56: Generated 1 of the 1 non-bonded parameter combinations
56:
56: Excluding 1 bonded neighbours molecule type 'Dipole'
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200
56:
56: Estimate for the relative computational load of the PME mesh part: 1.00
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.955 0.478 199.9
56: (ns/day) (hour/ns)
56: Performance: 9.492 2.528
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Last energy frame read 5 time 0.050
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (16652 ms)
56: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (56234 ms total)
56:
56: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest
56: No protocol specified
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -1187121321
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.444 0.222 199.8
56: (ns/day) (hour/ns)
56: Performance: 1.943 12.350
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -1092824226
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.342 0.171 199.8
56: (ns/day) (hour/ns)
56: Performance: 2.526 9.503
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (23910 ms)
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to 1935699833
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.317 0.159 199.7
56: (ns/day) (hour/ns)
56: Performance: 2.722 8.817
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -1478525297
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.324 0.162 199.7
56: (ns/day) (hour/ns)
56: Performance: 2.660 9.022
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (432 ms)
56: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (24342 ms total)
56:
56: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest
56: No protocol specified
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0
56: Generating 1-4 interactions: fudge = 0.5
56: Pull group 1 'FirstWaterMolecule' has 3 atoms
56: Pull group 2 'SecondWaterMolecule' has 3 atoms
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56: Pull group natoms pbc atom distance at start reference at t=0
56: 1 3 2
56: 2 3 5 1.112 nm 1.000 nm
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'spc2'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -247349505
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Generated 3 of the 3 1-4 parameter combinations
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.497 0.248 199.9
56: (ns/day) (hour/ns)
56: Performance: 1.738 13.805
56: Generating 1-4 interactions: fudge = 0.5
56: Pull group 1 'FirstWaterMolecule' has 3 atoms
56: Pull group 2 'SecondWaterMolecule' has 3 atoms
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56: Pull group natoms pbc atom distance at start reference at t=0
56: 1 3 2
56: 2 3 5 1.112 nm 1.000 nm
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'spc2'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -545405091
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Generated 3 of the 3 1-4 parameter combinations
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.514 0.257 199.9
56: (ns/day) (hour/ns)
56: Performance: 1.679 14.296
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (543 ms)
56: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (543 ms total)
56:
56: [----------] Global test environment tear-down
56: [==========] 14 tests from 6 test cases ran. (86341 ms total)
56: [ PASSED ] 14 tests.
56/65 Test #56: MdrunTests ............................ Passed 86.37 sec
test 57
Start 57: MdrunPmeTests
57: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-pme-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunPmeTests.xml"
57: Test timeout computed to be: 600
57: [==========] Running 3 tests from 1 test case.
57: [----------] Global test environment set-up.
57: [----------] 3 tests from PmeTest
57: No protocol specified
57: [ RUN ] PmeTest.ReproducesEnergies
57: Number of degrees of freedom in T-Coupling group rest is 12.00
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
57: NVE simulation: will use the initial temperature of 1046.791 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 2 notes
57: No protocol specified
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57: Setting the LD random seed to -1008836883
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.448 0.224 199.9
57: (ns/day) (hour/ns)
57: Performance: 8.104 2.962
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.380 0.190 199.9
57: (ns/day) (hour/ns)
57: Performance: 9.551 2.513
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57:
57: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.328 0.164 199.8
57: (ns/day) (hour/ns)
57: Performance: 11.056 2.171
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10881 ms)
57: [ RUN ] PmeTest.ScalesTheBox
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: For a correct single-point energy evaluation with nsteps = 0, use
57: continuation = yes to avoid constraining the input coordinates.
57:
57: Number of degrees of freedom in T-Coupling group rest is 12.00
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: NVE simulation: will use the initial temperature of 1046.791 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 3 notes
57: No protocol specified
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 0 steps, 0.0 ps.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.004 0.002 185.9
57: (ns/day) (hour/ns)
57: Performance: 40.590 0.591
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1928659329
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57: [ OK ] PmeTest.ScalesTheBox (52 ms)
57: [ RUN ] PmeTest.ScalesTheBoxWithWalls
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: For a correct single-point energy evaluation with nsteps = 0, use
57: continuation = yes to avoid constraining the input coordinates.
57:
57: Number of degrees of freedom in T-Coupling group rest is 13.00
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: NVE simulation: will use the initial temperature of 966.268 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 3 notes
57: No protocol specified
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 0 steps, 0.0 ps.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.015 0.007 194.7
57: (ns/day) (hour/ns)
57: Performance: 11.590 2.071
57: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
57:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1912735761
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Searching the wall atom type(s)
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57: [ OK ] PmeTest.ScalesTheBoxWithWalls (30863 ms)
57: [----------] 3 tests from PmeTest (41797 ms total)
57:
57: [----------] Global test environment tear-down
57: [==========] 3 tests from 1 test case ran. (41820 ms total)
57: [ PASSED ] 3 tests.
57/65 Test #57: MdrunPmeTests ......................... Passed 41.85 sec
test 58
Start 58: MdrunNonIntegratorTests
58: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml"
58: Test timeout computed to be: 600
58: [==========] Running 58 tests from 5 test cases.
58: [----------] Global test environment set-up.
58: [----------] 1 test from NonbondedBenchTest
58: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
58: System size: 3000 atoms
58: Cut-off radius: 1 nm
58: Number of threads: 1
58: Number of iterations: 1
58: Compute energies: no
58: Ewald excl. corr.: analytical
58:
58: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
58: total useful
58: Ewald all geom. no 0.000 0.0000 inf inf
58: [ OK ] NonbondedBenchTest.BasicEndToEndTest (253 ms)
58: [----------] 1 test from NonbondedBenchTest (254 ms total)
58:
58: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
58: No protocol specified
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -4.7990997e+01
58: Maximum force = 1.8629761e+02 on atom 13
58: Norm of force = 8.7722009e+01
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1726 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 3.02331e+02 on atom 3
58: F-Norm = 1.18024e+02
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -5.5862339e+01
58: Maximum force = 4.2727011e+02 on atom 13
58: Norm of force = 1.8452841e+02
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1711 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 22.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 3.1937714e+02
58: Maximum force = 9.9988643e+03 on atom 9
58: Norm of force = 4.6166996e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: turning H bonds into constraints...
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (405 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58:
58: NOTE 3 [file glycine_vacuo.top, line 12]:
58: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
58:
58: Number of degrees of freedom in T-Coupling group System is 22.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 2.41575e+04 on atom 10
58: F-Norm = 1.18451e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 1.5174377e+02
58: Maximum force = 7.4208838e+03 on atom 9
58: Norm of force = 3.5693005e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: turning H bonds into constraints...
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (408 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -1.5698413e+02
58: Maximum force = 4.5704984e+02 on atom 17
58: Norm of force = 1.8327747e+02
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (51 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58:
58: NOTE 4 [file unknown]:
58: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 1.06801e+03 on atom 28
58: F-Norm = 4.26916e+02
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -1.6941180e+02
58: Maximum force = 2.1832491e+02 on atom 17
58: Norm of force = 7.9220732e+01
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (51 ms)
58: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (4353 ms total)
58:
58: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
58: No protocol specified
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents converged to Fmax < 10 in 1 steps
58: Potential Energy = -9.7425699e-01
58: Maximum force = 4.0132303e+00 on atom 1
58: Norm of force = 1.6383944e+00
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (17 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 4.01323e+00 on atom 1
58: F-Norm = 1.63839e+00
58:
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
58: Potential Energy = -9.9064207e-01
58: Maximum force = 2.5781622e+00 on atom 1
58: Norm of force = 1.0525302e+00
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (18 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58:
58: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58:
58: There was 1 warning
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Low-Memory BFGS Minimizer:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: Using 10 BFGS correction steps.
58:
58: F-max = 4.01323e+00 on atom 1
58: F-Norm = 1.63839e+00
58:
58:
58: writing lowest energy coordinates.
58:
58: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
58: Potential Energy = -9.9064207e-01
58: Maximum force = 2.5781622e+00 on atom 1
58: Norm of force = 1.0525302e+00
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (18 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 3.1939697e+02
58: Maximum force = 9.9704248e+03 on atom 9
58: Norm of force = 4.6227540e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (403 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 2.41672e+04 on atom 10
58: F-Norm = 1.19357e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 1.5625757e+02
58: Maximum force = 7.5018242e+03 on atom 9
58: Norm of force = 3.6139019e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (403 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58:
58: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58:
58: There was 1 warning
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Low-Memory BFGS Minimizer:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: Using 10 BFGS correction steps.
58:
58: F-max = 2.41672e+04 on atom 10
58: F-Norm = 1.19357e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 5.6111725e+02
58: Maximum force = 1.2685491e+04 on atom 10
58: Norm of force = 6.0643622e+03
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (405 ms)
58: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1264 ms total)
58:
58: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
58: No protocol specified
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 68.810 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.410 0.205 199.9
58: (ns/day) (hour/ns)
58: Performance: 7.162 3.351
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
58:
58: trr version: GMX_trn_file (single precision)
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.003 0.002 192.4
58: (ns/day) (hour/ns)
58: Performance: 881.849 0.027
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (231 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 68.810 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.330 0.165 199.9
58: (ns/day) (hour/ns)
58: Performance: 8.902 2.696
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.003 0.002 191.8
58: (ns/day) (hour/ns)
58: Performance: 888.078 0.027
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (192 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.375 0.188 199.9
58: (ns/day) (hour/ns)
58: Performance: 7.824 3.067
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.003 0.002 192.0
58: (ns/day) (hour/ns)
58: Performance: 942.419 0.025
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (226 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.369 0.185 199.9
58: (ns/day) (hour/ns)
58: Performance: 7.951 3.019
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 194.5
58: (ns/day) (hour/ns)
58: Performance: 461.918 0.052
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (236 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: NVE simulation: will use the initial temperature of 398.997 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.458 0.229 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.405 3.747
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.003 0.002 192.1
58: (ns/day) (hour/ns)
58: Performance: 898.308 0.027
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (1982 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: NVE simulation: will use the initial temperature of 398.997 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.484 0.242 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.067 3.956
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.003 0.002 192.1
58: (ns/day) (hour/ns)
58: Performance: 911.735 0.026
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (1951 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.389 0.194 199.9
58: (ns/day) (hour/ns)
58: Performance: 7.552 3.178
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.003 0.002 172.5
58: (ns/day) (hour/ns)
58: Performance: 781.405 0.031
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (1895 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.481 0.241 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.104 3.932
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.003 0.002 192.3
58: (ns/day) (hour/ns)
58: Performance: 886.927 0.027
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (1960 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: NVE simulation: will use the initial temperature of 456.887 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 6 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.416 0.208 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.054 3.402
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 193.8
58: (ns/day) (hour/ns)
58: Performance: 578.840 0.041
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (275 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: NVE simulation: will use the initial temperature of 456.887 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 6 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.369 0.185 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.947 3.020
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 194.1
58: (ns/day) (hour/ns)
58: Performance: 576.187 0.042
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (250 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.412 0.206 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.128 3.367
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 193.7
58: (ns/day) (hour/ns)
58: Performance: 578.622 0.041
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (310 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.386 0.193 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.599 3.158
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 193.9
58: (ns/day) (hour/ns)
58: Performance: 563.589 0.043
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (285 ms)
58: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (9794 ms total)
58:
58: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
58: No protocol specified
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.486 0.243 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.042 3.972
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 185.0
58: (ns/day) (hour/ns)
58: Performance: 449.514 0.053
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (308 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.400 0.200 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.328 3.275
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 186.5
58: (ns/day) (hour/ns)
58: Performance: 453.819 0.053
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (266 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.468 0.234 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.268 3.829
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.004 185.8
58: (ns/day) (hour/ns)
58: Performance: 404.663 0.059
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (300 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.515 0.258 199.8
58: (ns/day) (hour/ns)
58: Performance: 5.701 4.210
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.004 184.6
58: (ns/day) (hour/ns)
58: Performance: 417.187 0.058
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (324 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.629 0.315 199.8
58: (ns/day) (hour/ns)
58: Performance: 4.666 5.143
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.004 187.6
58: (ns/day) (hour/ns)
58: Performance: 415.134 0.058
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (382 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.465 0.233 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.313 3.802
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 184.7
58: (ns/day) (hour/ns)
58: Performance: 649.509 0.037
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (293 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.521 0.261 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.633 4.260
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 185.0
58: (ns/day) (hour/ns)
58: Performance: 631.144 0.038
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (309 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.512 0.256 199.8
58: (ns/day) (hour/ns)
58: Performance: 5.732 4.187
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 186.4
58: (ns/day) (hour/ns)
58: Performance: 458.003 0.052
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (311 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.617 0.309 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.759 5.043
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 185.1
58: (ns/day) (hour/ns)
58: Performance: 650.538 0.037
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (368 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.440 0.220 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.675 3.596
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 185.3
58: (ns/day) (hour/ns)
58: Performance: 618.596 0.039
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (266 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.439 0.220 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.677 3.594
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 184.0
58: (ns/day) (hour/ns)
58: Performance: 453.986 0.053
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (271 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.484 0.242 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.067 3.956
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 185.1
58: (ns/day) (hour/ns)
58: Performance: 653.783 0.037
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (302 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.776 0.388 200.0
58: (ns/day) (hour/ns)
58: Performance: 3.782 6.345
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 184.6
58: (ns/day) (hour/ns)
58: Performance: 642.063 0.037
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (440 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.438 0.219 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.701 3.581
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 185.9
58: (ns/day) (hour/ns)
58: Performance: 624.300 0.038
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (266 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.540 0.270 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.440 4.412
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 185.0
58: (ns/day) (hour/ns)
58: Performance: 649.783 0.037
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (315 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.501 0.250 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.864 4.093
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 186.4
58: (ns/day) (hour/ns)
58: Performance: 456.340 0.053
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (313 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.452 0.226 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.503 3.691
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 186.3
58: (ns/day) (hour/ns)
58: Performance: 450.566 0.053
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (291 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.657 0.328 200.0
58: (ns/day) (hour/ns)
58: Performance: 4.471 5.367
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 185.1
58: (ns/day) (hour/ns)
58: Performance: 646.985 0.037
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (377 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.490 0.245 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.989 4.007
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 185.0
58: (ns/day) (hour/ns)
58: Performance: 648.552 0.037
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (290 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.425 0.212 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.914 3.471
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 184.6
58: (ns/day) (hour/ns)
58: Performance: 643.337 0.037
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (258 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.472 0.236 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.221 3.858
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 186.4
58: (ns/day) (hour/ns)
58: Performance: 448.043 0.054
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (287 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.461 0.230 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.373 3.766
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 186.2
58: (ns/day) (hour/ns)
58: Performance: 454.020 0.053
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (283 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.486 0.243 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.043 3.971
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 186.2
58: (ns/day) (hour/ns)
58: Performance: 587.283 0.041
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (329 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.433 0.217 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.781 3.539
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 189.4
58: (ns/day) (hour/ns)
58: Performance: 440.231 0.055
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (306 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.432 0.216 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.794 3.533
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.004 187.2
58: (ns/day) (hour/ns)
58: Performance: 418.036 0.057
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (302 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.458 0.229 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.402 3.749
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.002 185.7
58: (ns/day) (hour/ns)
58: Performance: 592.764 0.040
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (297 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.559 0.280 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.252 4.570
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.002 186.1
58: (ns/day) (hour/ns)
58: Performance: 590.548 0.041
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (365 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.493 0.247 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.952 4.032
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 186.2
58: (ns/day) (hour/ns)
58: Performance: 575.918 0.042
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (316 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.461 0.231 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.365 3.771
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 186.2
58: (ns/day) (hour/ns)
58: Performance: 679.977 0.035
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (306 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.464 0.232 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.328 3.792
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.002 185.5
58: (ns/day) (hour/ns)
58: Performance: 604.098 0.040
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (308 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.599 0.300 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.903 4.895
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.002 185.7
58: (ns/day) (hour/ns)
58: Performance: 594.996 0.040
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (366 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.399 0.200 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.349 3.266
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 185.4
58: (ns/day) (hour/ns)
58: Performance: 606.835 0.040
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (266 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.483 0.242 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.081 3.947
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 185.3
58: (ns/day) (hour/ns)
58: Performance: 614.891 0.039
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (310 ms)
58: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (10294 ms total)
58:
58: [----------] Global test environment tear-down
58: [==========] 58 tests from 5 test cases ran. (26047 ms total)
58: [ PASSED ] 58 tests.
58/65 Test #58: MdrunNonIntegratorTests ............... Passed 26.08 sec
test 59
Start 59: MdrunTpiTests
59: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTpiTests.xml"
59: Test timeout computed to be: 600
59: [==========] Running 2 tests from 1 test case.
59: [----------] Global test environment set-up.
59: [----------] 2 tests from Simple/TpiTest
59: No protocol specified
59: [ RUN ] Simple/TpiTest.ReproducesOutput/0
59: Ignoring obsolete mdp entry 'ns_type'
59: Generating 1-4 interactions: fudge = 0.5
59: Number of degrees of freedom in T-Coupling group System is 1308.00
59: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
59: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
59: TPI is not implemented for GPUs.
59:
59: Using 1 MPI thread
59: Using 1 OpenMP thread
59:
59:
59: NOTE: Thread affinity was not set.
59:
59: WARNING: Using the slow plain C kernels. This should
59: not happen during routine usage on supported platforms.
59: Reading frames from gro file '216 water molecules', 648 atoms.
59:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
59:
Last frame 0 time 0.000
59: Generated 331705 of the 331705 non-bonded parameter combinations
59:
59: Generated 331705 of the 331705 1-4 parameter combinations
59:
59: Excluding 2 bonded neighbours molecule type 'SOL'
59:
59: Excluding 3 bonded neighbours molecule type 'methane'
59: Analysing residue names:
59: There are: 216 Water residues
59: There are: 1 Other residues
59: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
59:
59: This run will generate roughly 0 Mb of data
59: [ OK ] Simple/TpiTest.ReproducesOutput/0 (1787 ms)
59: [ RUN ] Simple/TpiTest.ReproducesOutput/1
59: Ignoring obsolete mdp entry 'ns_type'
59: Generating 1-4 interactions: fudge = 0.5
59: Number of degrees of freedom in T-Coupling group System is 1308.00
59: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
59: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
59: TPI is not implemented for GPUs.
59:
59: Using 1 MPI thread
59: Using 1 OpenMP thread
59:
59:
59: NOTE: Thread affinity was not set.
59:
59: WARNING: Using the slow plain C kernels. This should
59: not happen during routine usage on supported platforms.
59: Reading frames from gro file '216 water molecules', 648 atoms.
59:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
59:
Last frame 0 time 0.000
59: Generated 331705 of the 331705 non-bonded parameter combinations
59:
59: Generated 331705 of the 331705 1-4 parameter combinations
59:
59: Excluding 2 bonded neighbours molecule type 'SOL'
59:
59: Excluding 3 bonded neighbours molecule type 'methane'
59: Analysing residue names:
59: There are: 216 Water residues
59: There are: 1 Other residues
59: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
59:
59: This run will generate roughly 0 Mb of data
59: [ OK ] Simple/TpiTest.ReproducesOutput/1 (1852 ms)
59: [----------] 2 tests from Simple/TpiTest (3639 ms total)
59:
59: [----------] Global test environment tear-down
59: [==========] 2 tests from 1 test case ran. (3655 ms total)
59: [ PASSED ] 2 tests.
59/65 Test #59: MdrunTpiTests ......................... Passed 3.68 sec
test 60
Start 60: MdrunMpiTests
60: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiTests.xml"
60: Test timeout computed to be: 600
60: [==========] Running 22 tests from 7 test cases.
60: [----------] Global test environment set-up.
60: [----------] 1 test from DomainDecompositionSpecialCasesTest
60: No protocol specified
60: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 9.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc2'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.002 0.001 293.8
60: (ns/day) (hour/ns)
60: Performance: 105.453 0.228
60: Setting the LD random seed to 1471402583
60:
60: Generated 3 of the 3 non-bonded parameter combinations
60:
60: Generated 3 of the 3 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (22 ms)
60: [----------] 1 test from DomainDecompositionSpecialCasesTest (23 ms total)
60:
60: [----------] 4 tests from MimicTest
60: No protocol specified
60: [ RUN ] MimicTest.OneQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.519 0.660 381.8
60: (ns/day) (hour/ns)
60: Performance: 0.131 183.282
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 1743584254
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.OneQuantumMol (2081 ms)
60: [ RUN ] MimicTest.AllQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.538 0.664 381.9
60: (ns/day) (hour/ns)
60: Performance: 0.130 184.549
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -536880641
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.AllQuantumMol (2059 ms)
60: [ RUN ] MimicTest.TwoQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.399 0.630 380.9
60: (ns/day) (hour/ns)
60: Performance: 0.137 174.947
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -538454537
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.TwoQuantumMol (2028 ms)
60: [ RUN ] MimicTest.BondCuts
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 66.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: NVE simulation: will use the initial temperature of 300.368 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
60:
60: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.279 0.600 380.0
60: (ns/day) (hour/ns)
60: Performance: 0.144 166.631
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1074872329
60:
60: Generated 2211 of the 2211 non-bonded parameter combinations
60:
60: Generated 2211 of the 2211 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.BondCuts (2001 ms)
60: [----------] 4 tests from MimicTest (8174 ms total)
60:
60: [----------] 1 test from MultiSimTerminationTest
60: No protocol specified
60: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
60: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
60: [----------] 1 test from MultiSimTerminationTest (0 ms total)
60:
60: [----------] 1 test from ReplicaExchangeTerminationTest
60: No protocol specified
60: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
60: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
60: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
60:
60: [----------] 3 tests from PmeTest
60: No protocol specified
60: [ RUN ] PmeTest.ReproducesEnergies
60: Number of degrees of freedom in T-Coupling group rest is 12.00
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
60: NVE simulation: will use the initial temperature of 1046.791 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 2 notes
60: No protocol specified
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60: Setting the LD random seed to 2138852351
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 5.390 1.390 387.8
60: (ns/day) (hour/ns)
60: Performance: 1.306 18.384
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 5.750 1.480 388.5
60: (ns/day) (hour/ns)
60: Performance: 1.226 19.576
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 5.837 1.500 389.2
60: (ns/day) (hour/ns)
60: Performance: 1.210 19.837
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (27474 ms)
60: [ RUN ] PmeTest.ScalesTheBox
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Number of degrees of freedom in T-Coupling group rest is 12.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: NVE simulation: will use the initial temperature of 1046.791 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 3 notes
60: No protocol specified
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.222 0.095 234.3
60: (ns/day) (hour/ns)
60: Performance: 0.910 26.367
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1078559619
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] PmeTest.ScalesTheBox (999 ms)
60: [ RUN ] PmeTest.ScalesTheBoxWithWalls
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Number of degrees of freedom in T-Coupling group rest is 13.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: NVE simulation: will use the initial temperature of 966.268 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 3 notes
60: No protocol specified
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.360 0.130 277.4
60: (ns/day) (hour/ns)
60: Performance: 0.665 36.081
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -67144877
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Searching the wall atom type(s)
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] PmeTest.ScalesTheBoxWithWalls (64130 ms)
60: [----------] 3 tests from PmeTest (92604 ms total)
60:
60: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
60: No protocol specified
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -4.7990929e+01
60: Maximum force = 1.8629704e+02 on atom 13
60: Norm of force = 8.7721907e+01
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
60:
60: Generated 330891 of the 330891 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (4558 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 3.02331e+02 on atom 3
60: F-Norm = 1.18024e+02
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -5.5862312e+01
60: Maximum force = 4.2726910e+02 on atom 13
60: Norm of force = 1.8452761e+02
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
60:
60: Generated 330891 of the 330891 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (6070 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 22.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 3.1937704e+02
60: Maximum force = 9.9988633e+03 on atom 9
60: Norm of force = 4.6166993e+03
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: turning H bonds into constraints...
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (3290 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60:
60: NOTE 3 [file glycine_vacuo.top, line 12]:
60: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
60:
60: Number of degrees of freedom in T-Coupling group System is 22.00
60:
60: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 4 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 2.41575e+04 on atom 10
60: F-Norm = 1.18451e+04
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 1.5174442e+02
60: Maximum force = 7.4208892e+03 on atom 9
60: Norm of force = 3.5693002e+03
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: turning H bonds into constraints...
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (4930 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60:
60: NOTE 3 [file unknown]:
60: You are using constraints on all bonds, whereas the forcefield has been
60: parametrized only with constraints involving hydrogen atoms. We suggest
60: using constraints = h-bonds instead, this will also improve performance.
60:
60: Number of degrees of freedom in T-Coupling group System is 23.00
60:
60: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 4 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -1.5698419e+02
60: Maximum force = 4.5704996e+02 on atom 17
60: Norm of force = 1.8327748e+02
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations
60:
60: Generated 2145 of the 2145 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
60:
60: turning all bonds into constraints...
60:
60: Cleaning up constraints and constant bonded interactions with virtual sites
60:
60: Removed 18 Angles with virtual sites, 21 left
60:
60: Removed 10 Proper Dih.s with virtual sites, 44 left
60:
60: Converted 15 Constraints with virtual sites to connections, 7 left
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (4131 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60:
60: NOTE 3 [file unknown]:
60: You are using constraints on all bonds, whereas the forcefield has been
60: parametrized only with constraints involving hydrogen atoms. We suggest
60: using constraints = h-bonds instead, this will also improve performance.
60:
60:
60: NOTE 4 [file unknown]:
60: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
60:
60: Number of degrees of freedom in T-Coupling group System is 23.00
60:
60: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 5 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 1.06801e+03 on atom 28
60: F-Norm = 4.26916e+02
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -1.6941193e+02
60: Maximum force = 2.1835349e+02 on atom 17
60: Norm of force = 7.9216550e+01
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations
60:
60: Generated 2145 of the 2145 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
60:
60: turning all bonds into constraints...
60:
60: Cleaning up constraints and constant bonded interactions with virtual sites
60:
60: Removed 18 Angles with virtual sites, 21 left
60:
60: Removed 10 Proper Dih.s with virtual sites, 44 left
60:
60: Converted 15 Constraints with virtual sites to connections, 7 left
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (6099 ms)
60: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (29078 ms total)
60:
60: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
60: No protocol specified
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents converged to Fmax < 10 in 1 steps
60: Potential Energy = -9.7425699e-01
60: Maximum force = 4.0132303e+00 on atom 3
60: Norm of force = 1.6383944e+00
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (1598 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 4.01323e+00 on atom 3
60: F-Norm = 1.63839e+00
60:
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
60: Potential Energy = -9.9064207e-01
60: Maximum force = 2.5781622e+00 on atom 3
60: Norm of force = 1.0525302e+00
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (2050 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60:
60: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60:
60: There was 1 warning
60: Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (7 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 3.1939685e+02
60: Maximum force = 9.9704248e+03 on atom 9
60: Norm of force = 4.6227568e+03
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (2884 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 2.41672e+04 on atom 10
60: F-Norm = 1.19357e+04
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 1.5625764e+02
60: Maximum force = 7.5018237e+03 on atom 9
60: Norm of force = 3.6139019e+03
60: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (4421 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60:
60: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60:
60: There was 1 warning
60: Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (310 ms)
60: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (11270 ms total)
60:
60: [----------] Global test environment tear-down
60: [==========] 22 tests from 7 test cases ran. (141301 ms total)
60: [ PASSED ] 22 tests.
60:
60: YOU HAVE 4 DISABLED TESTS
60:
60/65 Test #60: MdrunMpiTests ......................... Passed 141.34 sec
test 61
Start 61: MdrunMpiPmeTests
61: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiPmeTests.xml"
61: Test timeout computed to be: 600
61: [==========] Running 3 tests from 1 test case.
61: [----------] Global test environment set-up.
61: [----------] 3 tests from PmeTest
61: No protocol specified
61: [ RUN ] PmeTest.ReproducesEnergies
61: Number of degrees of freedom in T-Coupling group rest is 12.00
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
61: NVE simulation: will use the initial temperature of 1046.791 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 2 notes
61: No protocol specified
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61: Setting the LD random seed to 985372491
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 1.933 0.483 399.9
61: (ns/day) (hour/ns)
61: Performance: 3.754 6.394
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 5.766 1.485 388.3
61: (ns/day) (hour/ns)
61: Performance: 1.222 19.641
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61:
61: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 5.308 1.370 387.6
61: (ns/day) (hour/ns)
61: Performance: 1.325 18.116
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (15298 ms)
61: [ RUN ] PmeTest.ScalesTheBox
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: For a correct single-point energy evaluation with nsteps = 0, use
61: continuation = yes to avoid constraining the input coordinates.
61:
61: Number of degrees of freedom in T-Coupling group rest is 12.00
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: NVE simulation: will use the initial temperature of 1046.791 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 3 notes
61: No protocol specified
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 0 steps, 0.0 ps.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.280 0.110 254.9
61: (ns/day) (hour/ns)
61: Performance: 0.786 30.549
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 1886894943
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61: [ OK ] PmeTest.ScalesTheBox (1018 ms)
61: [ RUN ] PmeTest.ScalesTheBoxWithWalls
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: For a correct single-point energy evaluation with nsteps = 0, use
61: continuation = yes to avoid constraining the input coordinates.
61:
61: Number of degrees of freedom in T-Coupling group rest is 13.00
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: NVE simulation: will use the initial temperature of 966.268 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 3 notes
61: No protocol specified
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 0 steps, 0.0 ps.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.320 0.120 267.2
61: (ns/day) (hour/ns)
61: Performance: 0.721 33.299
61: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
61:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -153360661
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Searching the wall atom type(s)
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61: [ OK ] PmeTest.ScalesTheBoxWithWalls (62910 ms)
61: [----------] 3 tests from PmeTest (79227 ms total)
61:
61: [----------] Global test environment tear-down
61: [==========] 3 tests from 1 test case ran. (79250 ms total)
61: [ PASSED ] 3 tests.
61/65 Test #61: MdrunMpiPmeTests ...................... Passed 79.29 sec
test 62
Start 62: MdrunMpiCoordinationTestsOneRank
62: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
62: Test timeout computed to be: 1920
62: [==========] Running 39 tests from 3 test cases.
62: [----------] Global test environment set-up.
62: [----------] 1 test from BasicPropagators/PeriodicActionsTest
62: No protocol specified
62: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.461 0.461 100.0
62: (ns/day) (hour/ns)
62: Performance: 3.186 7.533
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.203 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.243 3.314
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.189 0.189 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.766 3.090
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.214 0.214 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.872 3.493
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.195 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.522 3.191
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.170 0.170 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.630 2.781
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1523 ms)
62: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1523 ms total)
62:
62: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest
62: No protocol specified
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.188 0.188 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.818 3.070
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.197 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.467 3.214
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.293 0.294 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.003 4.797
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.202 0.202 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.266 3.303
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.177 0.178 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.263 2.904
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.194 0.194 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.556 3.176
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1331 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.185 0.185 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.942 3.022
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.209 3.329
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.201 0.202 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.281 3.296
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.210 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.987 3.435
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.186 0.186 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.898 3.039
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.211 0.211 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.967 3.445
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1280 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.201 0.201 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.296 3.289
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.205 3.331
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.210 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.993 3.432
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.310 0.310 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.739 5.064
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.202 0.202 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.260 3.306
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.227 0.227 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.462 3.714
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1437 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.251 0.251 100.0
62: (ns/day) (hour/ns)
62: Performance: 5.848 4.104
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.212 0.212 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.915 3.471
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.206 3.331
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.276 0.277 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.312 4.518
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.186 0.186 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.890 3.042
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.894 3.481
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1437 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.201 0.201 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.295 3.290
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.178 0.179 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.223 2.919
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.210 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.995 3.431
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.202 0.202 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.270 3.301
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.177 0.178 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.269 2.903
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.202 0.202 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.258 3.307
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1255 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.201 0.201 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.298 3.289
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.170 0.170 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.625 2.783
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.218 0.218 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.724 3.570
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.202 0.202 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.277 3.298
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.211 0.211 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.967 3.445
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.186 0.186 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.899 3.038
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1271 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.218 0.218 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.740 3.561
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.279 0.279 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.267 4.557
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.211 0.212 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.930 3.463
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.210 0.210 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.984 3.437
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.203 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.234 3.318
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.211 0.212 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.940 3.458
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1428 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.193 0.193 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.610 3.154
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.212 0.212 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.915 3.471
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.294 0.294 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.995 4.805
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.219 0.219 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.703 3.581
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.196 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.506 3.197
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.898 3.479
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1424 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.176 0.176 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.349 2.875
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.189 0.189 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.760 3.093
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.211 0.211 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.971 3.443
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.211 0.211 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.966 3.445
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.195 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.532 3.186
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.179 0.180 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.181 2.934
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1287 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.202 0.202 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.263 3.304
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.197 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.473 3.212
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.170 0.170 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.641 2.777
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.251 0.251 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.851 4.102
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.194 0.195 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.549 3.179
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.178 0.178 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.248 2.910
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1309 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.202 0.202 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.281 3.296
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.197 3.335
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.179 0.179 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.213 2.922
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.183 3.341
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.205 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.176 3.344
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.188 0.188 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.805 3.075
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1254 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.195 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.533 3.186
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.205 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.151 3.356
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.171 0.171 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.583 2.796
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.220 0.221 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.656 3.606
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.196 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.487 3.206
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.304 0.305 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.818 4.981
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1365 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.179 0.179 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.206 2.925
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.206 0.206 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.122 3.370
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.206 0.206 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.127 3.368
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.206 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.145 3.359
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.230 0.230 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.373 3.766
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.198 3.334
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1359 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.169 0.169 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.668 2.769
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.206 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.146 3.358
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.192 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.641 3.141
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.202 0.202 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.256 3.308
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.202 0.203 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.237 3.316
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.221 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.642 3.613
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1387 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.195 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.516 3.193
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.216 0.217 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.781 3.539
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.187 3.339
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.191 3.337
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.898 3.479
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.288 0.288 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.103 4.703
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (1406 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.891 3.483
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.216 0.216 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.801 3.529
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.205 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.159 3.353
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.214 0.215 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.846 3.505
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.206 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.146 3.359
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.215 0.216 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.809 3.525
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1396 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.212 0.212 100.0
62: (ns/day) (hour/ns)
62: Performance: 6.928 3.464
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.215 0.215 100.0
62: (ns/day) (hour/ns)
62: Performance: 6.843 3.507
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.223 0.223 100.0
62: (ns/day) (hour/ns)
62: Performance: 6.580 3.647
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.221 100.0
62: (ns/day) (hour/ns)
62: Performance: 6.644 3.612
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.205 100.0
62: (ns/day) (hour/ns)
62: Performance: 7.172 3.346
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.263 0.263 100.0
62: (ns/day) (hour/ns)
62: Performance: 5.583 4.299
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (1435 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.303 0.303 100.0
62: (ns/day) (hour/ns)
62: Performance: 4.851 4.948
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.180 0.180 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.140 2.948
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.222 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.621 3.625
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.207 0.207 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.092 3.384
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.215 0.215 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.823 3.518
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.272 0.272 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.398 4.446
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (1498 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.212 0.212 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.922 3.467
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.214 0.214 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.851 3.503
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.207 0.207 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.090 3.385
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.306 0.306 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.799 5.001
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.207 0.207 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.089 3.385
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.207 0.207 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.099 3.381
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (1492 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.212 0.212 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.913 3.472
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.234 0.234 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.284 3.819
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.315 0.315 100.0
62: (ns/day) (hour/ns)
62: Performance: 4.660 5.150
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.231 0.232 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.342 3.785
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.198 0.199 100.0
62: (ns/day) (hour/ns)
62: Performance: 7.396 3.245
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.222 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.605 3.633
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (1541 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.303 0.303 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.840 4.958
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.217 0.217 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.760 3.550
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 1.206 1.206 100.0
62: (ns/day) (hour/ns)
62: Performance: 1.218 19.708
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.212 0.212 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.925 3.466
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.174 0.174 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.419 2.851
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.207 0.207 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.103 3.379
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (2472 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.196 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.510 3.196
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.308 0.309 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.759 5.043
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.198 0.198 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.414 3.237
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.198 0.199 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.392 3.247
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.223 0.223 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.577 3.649
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.206 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.146 3.358
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (1457 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.206 3.331
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.189 0.189 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.779 3.085
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.255 0.255 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.756 4.169
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.223 0.223 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.574 3.651
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.223 0.223 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.593 3.640
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.205 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.172 3.346
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (1409 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.196 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.489 3.204
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.214 0.214 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.866 3.495
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.228 0.229 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.422 3.737
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.211 0.211 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.967 3.445
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.195 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.534 3.186
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.303 0.303 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.848 4.950
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (1454 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.194 0.194 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.560 3.174
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.189 0.190 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.740 3.101
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.203 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.228 3.321
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.218 0.218 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.738 3.562
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.294 0.294 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.999 4.801
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.235 0.235 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.247 3.842
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (1464 ms)
62: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (35851 ms total)
62:
62: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest
62: No protocol specified
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.203 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.220 3.324
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.230 0.230 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.386 3.758
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.191 0.191 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.700 3.117
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.189 0.189 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.768 3.089
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.203 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.245 3.313
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.181 0.181 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.093 2.966
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (9128 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.179 0.179 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.223 2.919
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.169 0.170 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.662 2.771
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.181 0.181 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.104 2.961
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.192 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.635 3.143
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.160 0.160 99.9
62: (ns/day) (hour/ns)
62: Performance: 9.196 2.610
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.171 0.171 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.566 2.802
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (9656 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.230 0.231 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.368 3.769
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.159 0.159 99.9
62: (ns/day) (hour/ns)
62: Performance: 9.251 2.594
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.183 0.183 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.017 2.994
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.158 0.158 99.8
62: (ns/day) (hour/ns)
62: Performance: 9.297 2.581
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.184 0.184 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.967 3.012
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.186 0.186 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.886 3.043
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (10380 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.238 0.238 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.171 3.889
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.185 0.185 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.946 3.021
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.172 0.172 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.542 2.810
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.185 0.185 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.943 3.022
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.167 0.168 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.760 2.740
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.158 0.158 99.9
62: (ns/day) (hour/ns)
62: Performance: 9.305 2.579
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (10210 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.208 0.208 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.057 3.401
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.163 0.163 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.996 2.668
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.174 0.174 99.7
62: (ns/day) (hour/ns)
62: Performance: 8.428 2.848
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.197 0.197 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.456 3.219
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.197 0.197 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.461 3.217
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.183 0.183 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.032 2.988
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (10310 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.211 0.211 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.970 3.443
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.197 0.197 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.462 3.216
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.260 0.260 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.643 4.253
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.177 0.177 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.289 2.895
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.192 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.657 3.134
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.201 0.201 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.297 3.289
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (10733 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.229 0.229 100.0
62: (ns/day) (hour/ns)
62: Performance: 6.416 3.741
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.195 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.519 3.192
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.189 0.189 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.771 3.088
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.189 0.189 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.776 3.087
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.187 0.187 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.835 3.063
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.163 0.164 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.974 2.674
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (10913 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.234 0.234 100.0
62: (ns/day) (hour/ns)
62: Performance: 6.268 3.829
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.184 0.185 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.960 3.015
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.194 0.194 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.572 3.170
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.206 0.206 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.128 3.367
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.202 0.203 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.243 3.313
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.177 0.177 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.294 2.894
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (10759 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.217 0.217 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.760 3.551
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.278 0.279 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.271 4.553
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.163 0.163 99.8
62: (ns/day) (hour/ns)
62: Performance: 9.003 2.666
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.212 0.212 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.929 3.464
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.228 0.229 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.425 3.735
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.186 0.186 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.888 3.043
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (10840 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.218 0.218 100.0
62: (ns/day) (hour/ns)
62: Performance: 6.749 3.556
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.195 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.529 3.188
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.194 0.194 100.0
62: (ns/day) (hour/ns)
62: Performance: 7.571 3.170
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.175 0.176 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.367 2.868
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.166 0.167 100.0
62: (ns/day) (hour/ns)
62: Performance: 8.820 2.721
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 100.0
62: (ns/day) (hour/ns)
62: Performance: 6.883 3.487
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (10726 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.899 3.479
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.195 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.516 3.193
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.199 0.200 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.354 3.263
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.197 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.473 3.212
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.186 0.187 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.866 3.051
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.171 0.172 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.550 2.807
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (10724 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.179 0.179 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.205 2.925
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.192 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.653 3.136
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.231 0.231 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.351 3.779
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.201 0.201 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.291 3.292
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.218 0.218 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.747 3.557
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.890 3.483
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (10816 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.235 0.235 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.238 3.847
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.198 0.198 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.427 3.231
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.251 0.251 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.851 4.102
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.185 0.186 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.917 3.032
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.193 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.621 3.149
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.187 0.187 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.848 3.058
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (10874 ms)
62: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (136070 ms total)
62:
62: [----------] Global test environment tear-down
62: [==========] 39 tests from 3 test cases ran. (173509 ms total)
62: [ PASSED ] 39 tests.
62/65 Test #62: MdrunMpiCoordinationTestsOneRank ...... Passed 173.55 sec
test 63
Start 63: MdrunMpiCoordinationTestsTwoRanks
63: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml"
63: Test timeout computed to be: 1920
63: [==========] Running 39 tests from 3 test cases.
63: [----------] Global test environment set-up.
63: [----------] 1 test from BasicPropagators/PeriodicActionsTest
63: No protocol specified
63: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.397 0.199 199.8
63: (ns/day) (hour/ns)
63: Performance: 7.397 3.245
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.464 0.232 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.320 3.797
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.396 0.198 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.404 3.241
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.425 0.213 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.893 3.482
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.409 0.205 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.168 3.348
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.376 0.188 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.796 3.078
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1351 ms)
63: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1352 ms total)
63:
63: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest
63: No protocol specified
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.548 0.274 199.9
63: (ns/day) (hour/ns)
63: Performance: 5.358 4.480
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.413 0.207 199.8
63: (ns/day) (hour/ns)
63: Performance: 7.108 3.376
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.416 0.209 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.039 3.410
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.380 0.190 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.714 3.111
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.513 0.257 199.6
63: (ns/day) (hour/ns)
63: Performance: 5.710 4.203
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.483 0.242 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.066 3.957
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1566 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.394 0.197 199.8
63: (ns/day) (hour/ns)
63: Performance: 7.454 3.220
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.349 0.175 199.7
63: (ns/day) (hour/ns)
63: Performance: 8.400 2.857
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.446 0.223 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.578 3.649
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.429 0.215 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.829 3.514
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.397 0.199 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.380 3.252
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.380 0.190 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.712 3.112
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1303 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.561 0.281 199.8
63: (ns/day) (hour/ns)
63: Performance: 5.235 4.585
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.416 0.208 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.058 3.401
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.396 0.198 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.403 3.242
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.412 0.207 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.111 3.375
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.596 0.299 199.7
63: (ns/day) (hour/ns)
63: Performance: 4.919 4.879
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.413 0.207 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.097 3.382
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1504 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.428 0.214 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.856 3.501
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.416 0.208 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.051 3.404
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.429 0.215 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.835 3.511
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.579 0.290 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.070 4.734
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.413 0.207 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.097 3.382
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.207 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.088 3.386
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1445 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.394 0.197 199.8
63: (ns/day) (hour/ns)
63: Performance: 7.451 3.221
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.615 0.308 199.8
63: (ns/day) (hour/ns)
63: Performance: 4.773 5.028
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.396 0.198 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.414 3.237
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.413 0.207 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.108 3.377
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.364 0.182 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.058 2.978
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.430 0.216 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.815 3.522
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1412 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.577 0.289 199.8
63: (ns/day) (hour/ns)
63: Performance: 5.083 4.721
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.365 0.183 199.7
63: (ns/day) (hour/ns)
63: Performance: 8.026 2.990
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.379 0.190 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.744 3.099
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.447 0.224 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.560 3.659
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.382 0.191 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.684 3.123
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.365 0.183 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.040 2.985
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1363 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.602 0.301 199.8
63: (ns/day) (hour/ns)
63: Performance: 4.878 4.920
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 1.204 0.602 199.9
63: (ns/day) (hour/ns)
63: Performance: 2.439 9.842
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.430 0.215 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.828 3.515
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.430 0.215 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.816 3.521
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.381 0.191 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.701 3.117
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.365 0.183 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.038 2.986
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1811 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.395 0.198 199.8
63: (ns/day) (hour/ns)
63: Performance: 7.434 3.228
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.532 0.266 199.8
63: (ns/day) (hour/ns)
63: Performance: 5.515 4.352
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.430 0.215 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.822 3.518
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.447 0.224 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.562 3.658
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.346 0.173 199.5
63: (ns/day) (hour/ns)
63: Performance: 8.468 2.834
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.347 0.174 199.5
63: (ns/day) (hour/ns)
63: Performance: 8.438 2.844
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1354 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.544 0.272 199.9
63: (ns/day) (hour/ns)
63: Performance: 5.392 4.451
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.432 0.216 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.792 3.533
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.407 0.204 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.208 3.329
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.430 0.215 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.825 3.517
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.207 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.081 3.390
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.564 0.282 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.202 4.614
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1495 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.412 0.206 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.123 3.370
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.432 0.216 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.800 3.530
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.473 0.237 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.198 3.872
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.429 0.215 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.831 3.514
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.580 0.290 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.058 4.745
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63:
63: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Using Berendsen pressure coupling invalidates the true ensemble for the
63: thermostat
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63:
63: There was 1 warning
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.364 0.182 199.5
63: (ns/day) (hour/ns)
63: Performance: 8.061 2.977
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1446 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.361 0.181 199.8
63: (ns/day) (hour/ns)
63: Performance: 8.121 2.955
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.399 0.200 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.354 3.263
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.679 0.340 199.8
63: (ns/day) (hour/ns)
63: Performance: 4.321 5.554
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.396 0.198 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.403 3.242
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.430 0.216 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.815 3.522
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.207 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.085 3.387
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1445 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.394 0.197 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.439 3.226
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.515 0.258 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.696 4.214
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.463 0.232 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.338 3.787
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.589 0.295 199.7
63: (ns/day) (hour/ns)
63: Performance: 4.976 4.823
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.463 0.232 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.327 3.793
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.713 0.357 199.8
63: (ns/day) (hour/ns)
63: Performance: 4.115 5.832
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1670 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.395 0.198 199.8
63: (ns/day) (hour/ns)
63: Performance: 7.428 3.231
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.366 0.183 199.7
63: (ns/day) (hour/ns)
63: Performance: 8.016 2.994
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.380 0.190 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.715 3.111
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.630 0.315 199.8
63: (ns/day) (hour/ns)
63: Performance: 4.661 5.149
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.208 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.076 3.392
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.365 0.183 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.035 2.987
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1379 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.379 0.189 199.8
63: (ns/day) (hour/ns)
63: Performance: 7.752 3.096
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.416 0.208 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.057 3.401
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.563 0.282 199.8
63: (ns/day) (hour/ns)
63: Performance: 5.209 4.607
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.397 0.199 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.388 3.248
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.370 0.185 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.919 3.031
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.207 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.084 3.388
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1371 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.411 0.206 199.9
63: (ns/day) (hour/ns)
63: Performance: 7.141 3.361
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.525 0.263 199.8
63: (ns/day) (hour/ns)
63: Performance: 5.589 4.294
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.396 0.198 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.404 3.241
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.429 0.215 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.834 3.512
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.380 0.190 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.718 3.110
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.347 0.174 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.457 2.838
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (1346 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.543 0.272 199.8
63: (ns/day) (hour/ns)
63: Performance: 5.404 4.441
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.930 0.465 199.9
63: (ns/day) (hour/ns)
63: Performance: 3.155 7.606
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.378 0.189 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.759 3.093
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.363 0.182 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.085 2.969
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.513 0.257 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.712 4.201
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.447 0.224 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.556 3.661
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1694 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.395 0.198 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.417 3.236
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.400 0.200 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.332 3.273
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.696 0.348 199.8
63: (ns/day) (hour/ns)
63: Performance: 4.218 5.690
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.458 0.229 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.408 3.745
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.382 0.191 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.674 3.127
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.415 0.208 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.065 3.397
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (1471 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.478 0.239 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.143 3.907
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.565 0.283 199.8
63: (ns/day) (hour/ns)
63: Performance: 5.195 4.620
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.363 0.182 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.071 2.974
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.380 0.190 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.718 3.110
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.447 0.224 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.556 3.661
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.381 0.191 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.697 3.118
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (1412 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.577 0.289 199.8
63: (ns/day) (hour/ns)
63: Performance: 5.083 4.721
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.400 0.200 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.341 3.269
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.413 0.207 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.100 3.380
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.364 0.182 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.056 2.979
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.564 0.282 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.200 4.615
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
63: NVE simulation: will use the initial temperature of 68.810 K for
63: determining the Verlet buffer size
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.398 0.199 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.374 3.255
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (1462 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.412 0.206 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.115 3.373
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.566 0.283 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.183 4.630
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.613 0.307 199.7
63: (ns/day) (hour/ns)
63: Performance: 4.781 5.020
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.447 0.224 199.5
63: (ns/day) (hour/ns)
63: Performance: 6.552 3.663
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.445 0.223 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.589 3.642
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.481 0.241 199.6
63: (ns/day) (hour/ns)
63: Performance: 6.092 3.939
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (1587 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.411 0.206 199.8
63: (ns/day) (hour/ns)
63: Performance: 7.146 3.358
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.582 0.291 199.8
63: (ns/day) (hour/ns)
63: Performance: 5.043 4.759
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.397 0.199 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.393 3.246
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.207 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.088 3.386
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.381 0.191 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.696 3.118
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.580 0.291 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.055 4.748
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (1487 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.428 0.214 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.851 3.503
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.433 0.217 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.782 3.539
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.347 0.174 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.458 2.837
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.397 0.199 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.394 3.246
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.614 0.307 199.8
63: (ns/day) (hour/ns)
63: Performance: 4.779 5.022
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.207 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.082 3.389
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (1420 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.395 0.198 199.8
63: (ns/day) (hour/ns)
63: Performance: 7.426 3.232
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.432 0.216 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.791 3.534
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.457 0.229 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.419 3.739
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.563 0.282 199.8
63: (ns/day) (hour/ns)
63: Performance: 5.209 4.607
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.381 0.191 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.692 3.120
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.481 0.241 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.098 3.935
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (1454 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.411 0.206 199.8
63: (ns/day) (hour/ns)
63: Performance: 7.135 3.364
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.399 0.200 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.348 3.266
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.563 0.282 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.216 4.602
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.430 0.215 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.818 3.520
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.207 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.081 3.390
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.431 0.216 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.804 3.527
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (1429 ms)
63: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.760 0.380 199.9
63: (ns/day) (hour/ns)
63: Performance: 3.863 6.212
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.400 0.200 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.341 3.269
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.380 0.190 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.717 3.110
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.363 0.182 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.082 2.970
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.657 0.329 199.8
63: (ns/day) (hour/ns)
63: Performance: 4.467 5.372
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Number of degrees of freedom in T-Coupling group System is 33.00
63:
63: There were 2 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'Argon'
63: 16 steps, 0.0 ps.
63: Generated 1 of the 1 non-bonded parameter combinations
63:
63: Excluding 1 bonded neighbours molecule type 'Argon'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.414 0.207 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.079 3.390
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file
63: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (1587 ms)
63: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (36913 ms total)
63:
63: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest
63: No protocol specified
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.322 0.161 199.7
63: (ns/day) (hour/ns)
63: Performance: 9.124 2.631
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.347 0.174 199.7
63: (ns/day) (hour/ns)
63: Performance: 8.442 2.843
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.336 0.168 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.718 2.753
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.318 0.159 199.6
63: (ns/day) (hour/ns)
63: Performance: 9.212 2.605
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.417 0.209 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.036 3.411
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.558 0.279 199.8
63: (ns/day) (hour/ns)
63: Performance: 5.258 4.565
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (10846 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.370 0.185 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.931 3.026
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.308 0.154 199.5
63: (ns/day) (hour/ns)
63: Performance: 9.517 2.522
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.312 0.157 199.5
63: (ns/day) (hour/ns)
63: Performance: 9.380 2.559
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.323 0.162 199.5
63: (ns/day) (hour/ns)
63: Performance: 9.083 2.642
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.358 0.179 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.199 2.927
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.329 0.165 199.5
63: (ns/day) (hour/ns)
63: Performance: 8.911 2.693
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (10616 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.435 0.218 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.738 3.562
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.303 0.152 199.6
63: (ns/day) (hour/ns)
63: Performance: 9.678 2.480
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.309 0.155 199.4
63: (ns/day) (hour/ns)
63: Performance: 9.466 2.535
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.353 0.177 199.5
63: (ns/day) (hour/ns)
63: Performance: 8.299 2.892
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.400 0.200 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.333 3.273
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.300 0.150 199.4
63: (ns/day) (hour/ns)
63: Performance: 9.770 2.457
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (10874 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.650 0.325 199.9
63: (ns/day) (hour/ns)
63: Performance: 4.519 5.311
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.320 0.160 199.6
63: (ns/day) (hour/ns)
63: Performance: 9.166 2.618
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.316 0.158 199.4
63: (ns/day) (hour/ns)
63: Performance: 9.276 2.587
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.327 0.164 199.4
63: (ns/day) (hour/ns)
63: Performance: 8.970 2.676
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.358 0.179 199.5
63: (ns/day) (hour/ns)
63: Performance: 8.189 2.931
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.375 0.188 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.814 3.071
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (11115 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.488 0.244 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.013 3.991
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.357 0.179 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.208 2.924
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.387 0.194 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.558 3.176
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.401 0.201 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.300 3.288
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.370 0.186 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.916 3.032
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.394 0.197 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.443 3.224
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (11315 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.456 0.228 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.436 3.729
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.415 0.208 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.064 3.398
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.392 0.197 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.470 3.213
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.354 0.177 199.5
63: (ns/day) (hour/ns)
63: Performance: 8.281 2.898
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.342 0.172 199.3
63: (ns/day) (hour/ns)
63: Performance: 8.560 2.804
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.351 0.176 199.5
63: (ns/day) (hour/ns)
63: Performance: 8.343 2.877
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (11322 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.429 0.215 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.837 3.510
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.330 0.166 199.7
63: (ns/day) (hour/ns)
63: Performance: 8.873 2.705
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.475 0.238 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.176 3.886
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.361 0.181 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.131 2.952
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.362 0.182 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.090 2.967
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.311 0.156 199.6
63: (ns/day) (hour/ns)
63: Performance: 9.433 2.544
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (11222 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.441 0.221 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.659 3.604
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.355 0.178 199.7
63: (ns/day) (hour/ns)
63: Performance: 8.254 2.908
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.397 0.199 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.388 3.248
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.410 0.206 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.144 3.359
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.330 0.165 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.890 2.700
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.364 0.182 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.050 2.982
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (11198 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.474 0.237 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.185 3.880
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.416 0.208 199.7
63: (ns/day) (hour/ns)
63: Performance: 7.054 3.402
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.559 0.280 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.244 4.577
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.487 0.244 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.022 3.986
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.429 0.215 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.840 3.509
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.354 0.177 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.291 2.895
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (11497 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.544 0.273 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.389 4.453
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.333 0.167 199.4
63: (ns/day) (hour/ns)
63: Performance: 8.784 2.732
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.382 0.191 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.675 3.127
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.325 0.163 199.3
63: (ns/day) (hour/ns)
63: Performance: 9.019 2.661
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.384 0.193 199.4
63: (ns/day) (hour/ns)
63: Performance: 7.627 3.147
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.419 0.210 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.001 3.428
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (11305 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.487 0.244 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.024 3.984
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.381 0.191 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.698 3.118
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.357 0.179 199.5
63: (ns/day) (hour/ns)
63: Performance: 8.215 2.921
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.377 0.189 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.775 3.087
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.391 0.196 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.486 3.206
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: NVE simulation: will use the initial temperature of 398.997 K for
63: determining the Verlet buffer size
63:
63:
63: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 4 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Can not increase nstlist because an NVE ensemble is used
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.413 0.207 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.103 3.379
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (11322 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.514 0.257 199.7
63: (ns/day) (hour/ns)
63: Performance: 5.706 4.206
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.510 0.255 199.6
63: (ns/day) (hour/ns)
63: Performance: 5.752 4.172
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.397 0.199 199.5
63: (ns/day) (hour/ns)
63: Performance: 7.388 3.248
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.402 0.202 199.3
63: (ns/day) (hour/ns)
63: Performance: 7.283 3.295
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.450 0.225 199.4
63: (ns/day) (hour/ns)
63: Performance: 6.514 3.685
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.373 0.187 199.2
63: (ns/day) (hour/ns)
63: Performance: 7.845 3.059
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (11481 ms)
63: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.430 0.215 199.8
63: (ns/day) (hour/ns)
63: Performance: 6.830 3.514
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.488 0.244 199.7
63: (ns/day) (hour/ns)
63: Performance: 6.009 3.994
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.344 0.173 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.514 2.819
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.403 0.202 199.6
63: (ns/day) (hour/ns)
63: Performance: 7.268 3.302
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.356 0.179 199.6
63: (ns/day) (hour/ns)
63: Performance: 8.225 2.918
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63:
63: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
63: that with the Verlet scheme, nstlist has no effect on the accuracy of
63: your simulation.
63:
63:
63: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: Setting nstcalcenergy (100) equal to nstenergy (4)
63:
63: Generating 1-4 interactions: fudge = 0.5
63: Number of degrees of freedom in T-Coupling group System is 27.00
63:
63: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
63: You are using a plain Coulomb cut-off, which might produce artifacts.
63: You might want to consider using PME electrostatics.
63:
63:
63:
63: There were 3 notes
63: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
63: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
63: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
63:
63: Using 2 MPI threads
63: Using 1 OpenMP thread per tMPI thread
63:
63:
63: NOTE: The number of threads is not equal to the number of (logical) cores
63: and the -pin option is set to auto: will not pin threads to cores.
63: This can lead to significant performance degradation.
63: Consider using -pin on (and -pinoffset in case you run multiple jobs).
63:
63: WARNING: Using the slow plain C kernels. This should
63: not happen during routine usage on supported platforms.
63: starting mdrun 'spc2'
63: 16 steps, 0.0 ps.
63: Generated 330891 of the 330891 non-bonded parameter combinations
63:
63: Generated 330891 of the 330891 1-4 parameter combinations
63:
63: Excluding 2 bonded neighbours molecule type 'SOL'
63:
63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
63:
63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
63:
63: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
63:
63: Note that mdrun will redetermine rlist based on the actual pair-list setup
63:
63: This run will generate roughly 0 Mb of data
63:
63: Writing final coordinates.
63:
63: Core t (s) Wall t (s) (%)
63: Time: 0.358 0.179 199.3
63: (ns/day) (hour/ns)
63: Performance: 8.186 2.932
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
63: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
63: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (11438 ms)
63: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (145555 ms total)
63:
63: [----------] Global test environment tear-down
63: [==========] 39 tests from 3 test cases ran. (183884 ms total)
63: [ PASSED ] 39 tests.
63/65 Test #63: MdrunMpiCoordinationTestsTwoRanks ..... Passed 183.93 sec
test 64
Start 64: MdrunFEPTests
64: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunfep-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunFEPTests.xml"
64: Test timeout computed to be: 600
64: [==========] Running 10 tests from 1 test case.
64: [----------] Global test environment set-up.
64: [----------] 10 tests from FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest
64: No protocol specified
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]:
64: For proper sampling of the (nearly) decoupled state, stochastic dynamics
64: should be used
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -118761985
64:
64: Generated 153 of the 153 non-bonded parameter combinations
64:
64: Generated 153 of the 153 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64:
64: Coupling 1 copies of molecule type 'ASN'
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 1.250 0.625 199.9
64: (ns/day) (hour/ns)
64: Performance: 2.903 8.269
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision)
64: [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (10940 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]:
64: For proper sampling of the (nearly) decoupled state, stochastic dynamics
64: should be used
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -1879187482
64:
64: Generated 153 of the 153 non-bonded parameter combinations
64:
64: Generated 153 of the 153 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64:
64: Coupling 1 copies of molecule type 'ASN'
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 1.011 0.506 199.9
64: (ns/day) (hour/ns)
64: Performance: 3.586 6.692
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (594 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]:
64: For proper sampling of the (nearly) decoupled state, stochastic dynamics
64: should be used
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]:
64: With PME there is a minor soft core effect present at the cut-off,
64: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
64: energy conservation, but usually other effects dominate. With a common
64: sigma value of 0.34 nm the fraction of the particle-particle potential at
64: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06.
64:
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 5 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 5 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -1228952209
64:
64: Generated 153 of the 153 non-bonded parameter combinations
64:
64: Generated 153 of the 153 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64:
64: Coupling 1 copies of molecule type 'ASN'
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.616 0.308 199.9
64: (ns/day) (hour/ns)
64: Performance: 5.884 4.079
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (389 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]:
64: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off
64: and vdw_modifier=Force-switch
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 100 steps, 0.1 ps.
64: Setting the LD random seed to -1124122881
64:
64: Generated 153 of the 153 non-bonded parameter combinations
64:
64: Generated 153 of the 153 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64:
64: Coupling 1 copies of molecule type 'ASN'
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 1.548 0.774 199.9
64: (ns/day) (hour/ns)
64: Performance: 11.273 2.129
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Reading energy frame 30 time 0.030
Reading energy frame 40 time 0.040
Reading energy frame 50 time 0.050
Reading energy frame 60 time 0.060
Reading energy frame 70 time 0.070
Reading energy frame 80 time 0.080
Reading energy frame 90 time 0.090
Reading energy frame 100 time 0.100
Last energy frame read 100 time 0.100 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (863 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64:
64: WARNING 1 [file topol.top, line 72]:
64: No default Bond types for perturbed atoms, using normal values
64:
64:
64: WARNING 2 [file topol.top, line 73]:
64: No default Bond types for perturbed atoms, using normal values
64:
64:
64: WARNING 3 [file topol.top, line 98]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 4 [file topol.top, line 99]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 5 [file topol.top, line 100]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 6 [file topol.top, line 101]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 7 [file topol.top, line 111]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 8 [file topol.top, line 112]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 9 [file topol.top, line 113]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 10 [file topol.top, line 114]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 3 notes
64:
64: There were 10 warnings
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -135057938
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.871 0.436 199.9
64: (ns/day) (hour/ns)
64: Performance: 4.164 5.764
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (513 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64:
64: WARNING 1 [file topol.top, line 72]:
64: No default Bond types for perturbed atoms, using normal values
64:
64:
64: WARNING 2 [file topol.top, line 73]:
64: No default Bond types for perturbed atoms, using normal values
64:
64:
64: WARNING 3 [file topol.top, line 98]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 4 [file topol.top, line 99]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 5 [file topol.top, line 100]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 6 [file topol.top, line 101]:
64: No default Angle types for perturbed atoms, using normal values
64:
64:
64: WARNING 7 [file topol.top, line 111]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 8 [file topol.top, line 112]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 9 [file topol.top, line 113]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64:
64: WARNING 10 [file topol.top, line 114]:
64: No default Ryckaert-Bell. types for perturbed atoms, using normal values
64:
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 3 notes
64:
64: There were 10 warnings
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -33554997
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.784 0.392 199.9
64: (ns/day) (hour/ns)
64: Performance: 4.623 5.191
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (474 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 3 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to 1022866429
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.81
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.579 0.290 199.9
64: (ns/day) (hour/ns)
64: Performance: 6.258 3.835
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (358 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: There were 2 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64: Setting the LD random seed to -1208149057
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.81
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.655 0.328 199.8
64: (ns/day) (hour/ns)
64: Performance: 5.533 4.338
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (398 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]:
64: With PME there is a minor soft core effect present at the cut-off,
64: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
64: energy conservation, but usually other effects dominate. With a common
64: sigma value of 0.34 nm the fraction of the particle-particle potential at
64: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06.
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: Setting the LD random seed to -9981953
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.89
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.636 0.318 199.9
64: (ns/day) (hour/ns)
64: Performance: 5.705 4.207
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (394 ms)
64: [ RUN ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s
64:
64: NOTE 1 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]:
64: With PME there is a minor soft core effect present at the cut-off,
64: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
64: energy conservation, but usually other effects dominate. With a common
64: sigma value of 0.34 nm the fraction of the particle-particle potential at
64: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06.
64:
64:
64: NOTE 2 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]:
64: The Berendsen thermostat does not generate the correct kinetic energy
64: distribution. You might want to consider using the V-rescale thermostat.
64:
64: Generating 1-4 interactions: fudge = 0.5
64: Number of degrees of freedom in T-Coupling group System is 355.00
64:
64: NOTE 3 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]:
64: The optimal PME mesh load for parallel simulations is below 0.5
64: and for highly parallel simulations between 0.25 and 0.33,
64: for higher performance, increase the cut-off and the PME grid spacing.
64:
64:
64:
64: NOTE 4 [file /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]:
64: For free energy simulations, the optimal load limit increases from 0.5 to
64: 0.667
64:
64:
64:
64: There were 4 notes
64: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
64: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (single precision)
64: Changing nstlist from 10 to 100, rlist from 1 to 1
64:
64: Using 1 MPI thread
64: Using 2 OpenMP threads
64:
64:
64: NOTE: The number of threads is not equal to the number of (logical) cores
64: and the -pin option is set to auto: will not pin threads to cores.
64: This can lead to significant performance degradation.
64: Consider using -pin on (and -pinoffset in case you run multiple jobs).
64:
64: WARNING: Using the slow plain C kernels. This should
64: not happen during routine usage on supported platforms.
64: starting mdrun 'AA'
64: 20 steps, 0.0 ps.
64:
64: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
64: Setting the LD random seed to -1308697609
64:
64: Generated 136 of the 136 non-bonded parameter combinations
64:
64: Generated 136 of the 136 1-4 parameter combinations
64:
64: Excluding 3 bonded neighbours molecule type 'ASN'
64:
64: turning H bonds into constraints...
64:
64: Excluding 2 bonded neighbours molecule type 'SOL'
64:
64: turning H bonds into constraints...
64: Analysing residue names:
64: There are: 1 Protein residues
64: There are: 56 Water residues
64: Analysing Protein...
64:
64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
64:
64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
64:
64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
64:
64: Note that mdrun will redetermine rlist based on the actual pair-list setup
64: Calculating fourier grid dimensions for X Y Z
64: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
64:
64: Estimate for the relative computational load of the PME mesh part: 0.81
64:
64: This run will generate roughly 0 Mb of data
64:
64: Writing final coordinates.
64:
64: Core t (s) Wall t (s) (%)
64: Time: 0.543 0.272 199.9
64: (ns/day) (hour/ns)
64: Performance: 6.676 3.595
64: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file
64:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (339 ms)
64: [----------] 10 tests from FreeEnergyCalculationsAreEquivalentToReference/FreeEnergyReferenceTest (15268 ms total)
64:
64: [----------] Global test environment tear-down
64: [==========] 10 tests from 1 test case ran. (15292 ms total)
64: [ PASSED ] 10 tests.
64/65 Test #64: MdrunFEPTests ......................... Passed 15.32 sec
test 65
Start 65: MdrunSimulatorComparison
65: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml"
65: Test timeout computed to be: 600
65: [==========] Running 0 tests from 0 test cases.
65: [==========] 0 tests from 0 test cases ran. (0 ms total)
65: [ PASSED ] 0 tests.
65:
65: YOU HAVE 18 DISABLED TESTS
65:
65/65 Test #65: MdrunSimulatorComparison .............. Passed 0.03 sec
100% tests passed, 0 tests failed out of 65
Label Time Summary:
GTest = 894.67 sec*proc (63 tests)
IntegrationTest = 440.49 sec*proc (16 tests)
MpiTest = 578.32 sec*proc (8 tests)
SlowTest = 447.21 sec*proc (8 tests)
UnitTest = 6.97 sec*proc (39 tests)
Total Test time (real) = 895.04 sec
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:54:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/stl_vector.h:625:7: note: parameter passing for argument of type ‘std::initializer_list<double>’ changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/stl_vector.h:625:7: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
/<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp: In function ‘bool gmx::test::shouldDoComparison(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::test::ComparisonConditions)’:
/<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp:282:13: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
282 | static bool shouldDoComparison(ArrayRef<const RVec> values, ComparisonConditions comparisonConditions)
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function ‘virtual void gmx::test::{anonymous}::ConstraintsTest_SingleConstraint_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:315:51: note: parameter passing for argument of type ‘std::initializer_list<double>’ changed in GCC 7.1
315 | std::vector<real> masses = { 1.0, 12.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:317:45: note: parameter passing for argument of type ‘std::initializer_list<double>’ changed in GCC 7.1
317 | std::vector<real> constraintsR0 = { 0.1 };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.6.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function ‘virtual void gmx::test::{anonymous}::ConstraintsTest_TwoDisjointConstraints_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:376:5: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
376 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:380:5: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
380 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:382:104: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
382 | std::vector<RVec> v = { { 0.0, 1.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 0.0, 0.0, 1.0 }, { 0.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function ‘virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeSequentialConstraints_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:430:50: note: parameter passing for argument of type ‘std::initializer_list<double>’ changed in GCC 7.1
430 | std::vector<real> constraintsR0 = { 0.1, 0.2 };
| ^
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 68%] Built target testutils-test
/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function ‘virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeConstraintsWithCentralAtom_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:494:5: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
494 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:499:59: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
499 | { -0.005, 0.011, 0.102 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:501:104: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
501 | std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 } };
| ^
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function ‘virtual void gmx::test::{anonymous}::ConstraintsTest_FourSequentialConstraints_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:554:5: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
554 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:558:5: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
558 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:560:106: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
560 | std::vector<RVec> v = { { 0.0, 0.0, 2.0 }, { 0.0, 0.0, 3.0 }, { 0.0, 0.0, -4.0 }, { 0.0, 0.0, -1.0 } };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp: In member function ‘virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:234:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
234 | bias.calcForceAndUpdateBias(coordValue, {}, {}, &potential, &potentialJump, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
235 | nullptr, step, step, seed_, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:234:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:234:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:37:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘gmx::test::ConstraintsTestData::ConstraintsTestData(const string&, int, std::vector<double>, std::vector<int>, std::vector<double>, bool, real (*)[3], bool, float, real, real, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, real, gmx_bool, int, int, real)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp: In member function ‘virtual void gmx::test::BiasTest_DetectsCovering_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:319:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
319 | bias.calcForceAndUpdateBias(coordValue, {}, {}, &potential, &potentialJump, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
320 | nullptr, step, step, params.awhParams.seed, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:319:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias.cpp:319:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target mdrun_test_infrastructure
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasstate.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/dimparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasgrid.h:61,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasgrid.cpp:37:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::test::biasGridTest_neighborhood_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp: In member function ‘virtual void gmx::test::ShakeConstraintsRunner::applyConstraints(gmx::test::ConstraintsTestData*, t_pbc)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:87:35: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
87 | bool success = constrain_shake(
| ~~~~~~~~~~~~~~~^
88 | nullptr, &shaked, testData->invmass_.data(), *testData->idef_, testData->ir_, testData->x_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
89 | testData->xPrime_, testData->xPrime2_, nullptr, &testData->nrnb_, testData->lambda_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
90 | &testData->dHdLambda_, testData->invdt_, testData->v_, testData->computeVirial_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
91 | testData->virialScaled_, false, gmx::ConstraintVariable::Positions);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:87:35: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:87:35: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:87:35: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp: In member function ‘virtual void gmx::test::LincsConstraintsRunner::applyConstraints(gmx::test::ConstraintsTestData*, t_pbc)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:127:35: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
127 | bool success = constrain_lincs(
| ~~~~~~~~~~~~~~~^
128 | false, testData->ir_, 0, lincsd, testData->invmass_.data(), &cr, &ms,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
129 | testData->x_.arrayRefWithPadding(), testData->xPrime_.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | testData->xPrime2_.arrayRefWithPadding().unpaddedArrayRef(), pbc.box, &pbc,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | testData->hasMassPerturbed_, testData->lambda_, &testData->dHdLambda_, testData->invdt_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
132 | testData->v_.arrayRefWithPadding().unpaddedArrayRef(), testData->computeVirial_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
133 | testData->virialScaled_, gmx::ConstraintVariable::Positions, &testData->nrnb_, maxwarn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
134 | &warncount_lincs);
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp:127:35: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/biasstate.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/biasstate.cpp:37:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In constructor ‘gmx::test::BiasStateTest::BiasStateTest()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energydrifttracker.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::DimParams}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::DimParams>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In constructor ‘gmx::test::BiasFepLambdaStateTest::BiasFepLambdaStateTest()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp: In member function ‘virtual void gmx::test::BiasFepLambdaStateTest_ForcesBiasPmf_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:227:76: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
227 | gmx::ArrayRef<const double> biasForce = bias.calcForceAndUpdateBias(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^
228 | coordValue, neighborLambdaEnergies, neighborLambdaDhdl, &potential, &potentialJump,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | nullptr, nullptr, step * mdTimeStep, step, seed_, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:227:76: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:227:76: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:41:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::test::BiasFepLambdaStateTest_DetectsCovering_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:307:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
307 | bias.calcForceAndUpdateBias(coordValue, neighborLambdaEnergies, neighborLambdaDhdl,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
308 | &potential, &potentialJump, nullptr, nullptr, step, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
309 | params.awhParams.seed, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:307:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp:307:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target density_fitting_applied_forces-test
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/usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasgrid.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.6.0.0 ../../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target awh-test
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/expanded.cpp
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/11/bits/stl_vector.h: In function ‘static void gmx::test::{anonymous}::ElectricFieldTest::test(int, real, real, real, real, real)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target applied_forces-test
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target listed_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/freeenergyparameters.cpp
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:49:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::test::{anonymous}::iListInput; _Alloc = std::allocator<gmx::test::{anonymous}::iListInput>]’:
/usr/include/c++/11/bits/stl_vector.h:625:7: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:63,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:56:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<typename testing::internal::IteratorTraits<Iterator>::value_type> testing::ValuesIn(ForwardIterator, ForwardIterator) [with ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >]’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:304:1: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
304 | ValuesIn(ForwardIterator begin, ForwardIterator end) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:304:1: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_BondListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_BondZeroLengthListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_PolarizeListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_AngleListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_RestraintsListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_AngleZeroListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function ‘testing::internal::ParamGenerator<std::tuple<gmx::test::{anonymous}::iListInput, gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >, PbcType> > gmx::test::{anonymous}::gtest_DihedralListedForcesTest_EvalGenerator_()’:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:319:53: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::test::{anonymous}::iListInput*, std::vector<gmx::test::{anonymous}::iListInput> >’ changed in GCC 7.1
319 | return ValuesIn(container.begin(), container.end());
| ^
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:49:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:49:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘gmx::PaddedVector<T, Allocator>::PaddedVector(const std::initializer_list<_Tp>&) [with T = gmx::BasicVector<double>; Allocator = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’:
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:646:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
646 | std::vector<iListInput> c_InputBonds = {
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:661:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
661 | std::vector<iListInput> c_InputAngles = {
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:685:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
685 | std::vector<iListInput> c_InputDihs = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:695:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
695 | std::vector<iListInput> c_InputPols = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:705:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
705 | std::vector<iListInput> c_InputRestraints = {
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:715:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
715 | std::vector<iListInput> c_InputBondsZeroLength = {
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:720:25: note: parameter passing for argument of type ‘std::initializer_list<gmx::test::{anonymous}::iListInput>’ changed in GCC 7.1
720 | std::vector<iListInput> c_InputAnglesZeroAngle = {
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/listed_forces-test.dir/bonded.cpp.o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target listed_forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.6.0.0 ../../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target density_fitting_applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_grp_tcstat>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::test::LeapFrogHostTestRunner::integrate(gmx::test::LeapFrogTestData*, int)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target onlinehelp-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_iparams>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘gmx::test::SettleTestData::SettleTestData(int)’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/haloexchange_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::BasicVector<double>}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<gmx::BasicVector<double> > gmx::{anonymous}::computeDisplacements(gmx::ArrayRef<const int>, const std::vector<gmx::BasicVector<double> >&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp: In function ‘std::vector<double> gmx::{anonymous}::computeDistancesSquared(gmx::ArrayRef<const gmx::BasicVector<double> >)’:
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:109:19: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
109 | std::vector<real> computeDistancesSquared(ArrayRef<const RVec> displacements)
| ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<double> gmx::{anonymous}::computeHalfOfReducedMasses(const std::vector<int>&, const std::vector<double>&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ShakeTest::SetUp()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ShakeTest_ConstrainsThreeBondsWithCommonAtoms_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
198 | cshake(iatom.data(), numConstraints, &numIterations, ShakeTest::maxNumIterations_,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
199 | constrainedDistancesSquared, finalPositions, nullptr, initialDisplacements,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | halfOfReducedMasses, omega_, inverseMasses.data(), distanceSquaredTolerances,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | lagrangianValues, &numErrors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:204:93: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
204 | std::vector<real> finalDistancesSquared = computeDistancesSquared(finalDisplacements);
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/11/bits/vector.tcc: In function ‘static void gmx::{anonymous}::ShakeTest::runTest(size_t, size_t, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<gmx::BasicVector<double> >&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
198 | cshake(iatom.data(), numConstraints, &numIterations, ShakeTest::maxNumIterations_,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
199 | constrainedDistancesSquared, finalPositions, nullptr, initialDisplacements,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | halfOfReducedMasses, omega_, inverseMasses.data(), distanceSquaredTolerances,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | lagrangianValues, &numErrors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:204:93: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
204 | std::vector<real> finalDistancesSquared = computeDistancesSquared(finalDisplacements);
| ^
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoDisjointBonds_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoBondsWithACommonAtom_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ShakeTest_ConstrainsOneBond_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
198 | cshake(iatom.data(), numConstraints, &numIterations, ShakeTest::maxNumIterations_,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
199 | constrainedDistancesSquared, finalPositions, nullptr, initialDisplacements,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | halfOfReducedMasses, omega_, inverseMasses.data(), distanceSquaredTolerances,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | lagrangianValues, &numErrors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:198:15: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:204:93: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
204 | std::vector<real> finalDistancesSquared = computeDistancesSquared(finalDisplacements);
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target domdec-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target domdec-test
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
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/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_iparams>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::{anonymous}::UpdateGroups_butaneUA_Test::TestBody()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::{anonymous}::UpdateGroups_ethaneUA_Test::TestBody()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::{anonymous}::UpdateGroups_methane_Test::TestBody()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::{anonymous}::UpdateGroups_ethane_Test::TestBody()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::{anonymous}::UpdateGroups_waterThreeSite_Test::TestBody()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::{anonymous}::UpdateGroups_waterFourSite_Test::TestBody()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::{anonymous}::UpdateGroups_waterFlexAngle_Test::TestBody()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::{anonymous}::UpdateGroups_twoMoltypes_Test::TestBody()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_iparams>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void gmx::{anonymous}::UpdateGroupsCog_ComputesCogs_Test::TestBody()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
137 | updateGroupsCog.addCogs(globalAtomIndices, positions);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/listoflists.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target fft-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target mdlib-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mdmodulenotification-impl.cpp
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/stl_vector.h:625:7: note: parameter passing for argument of type ‘std::initializer_list<double>’ changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_availability.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’:
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:80:80: note: parameter passing for argument of type ‘std::initializer_list<double>’ changed in GCC 7.1
80 | 2.86F, 0.24F, 5.76F, 5.19F, 0.72F };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:119:1: note: parameter passing for argument of type ‘std::initializer_list<double>’ changed in GCC 7.1
119 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:147:1: note: parameter passing for argument of type ‘std::initializer_list<double>’ changed in GCC 7.1
147 | };
| ^
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_stream_manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/device_management.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/cpuinfo.cpp.o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/hardware-test.dir/device_management.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/range.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/range.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target hardware-test
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/strconvert.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; <template-parameter-2-2> = void; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/stl_vector.h:653:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
653 | vector(_InputIterator __first, _InputIterator __last,
| ^~~~~~
/usr/include/c++/11/bits/stl_vector.h:653:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’:
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:340:81: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
340 | c_sampleCoordinatesFull.begin() + 1);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:343:81: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
343 | c_sampleCoordinatesFull.begin() + 3);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:346:83: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
346 | c_sampleCoordinatesFull.begin() + 16);
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:58:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
111 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function ‘void gmx::test::runTest(const DeviceInformation&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]’:
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:101:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
101 | void runTest(const DeviceInformation& deviceInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:101:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
211 | runTest(testDevice->deviceInfo(), makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:58:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function ‘void gmx::test::runTest(const DeviceInformation&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]’:
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:101:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
101 | void runTest(const DeviceInformation& deviceInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:101:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
211 | runTest(testDevice->deviceInfo(), makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:211:16: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function ‘virtual void gmx::test::AffineTransformationTest_applyTransformationToVectors_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:215:85: note: parameter passing for argument of type ‘gmx::Matrix3x3ConstSpan’ {aka ‘gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >’} changed in GCC 7.1
215 | const AffineTransformation affineTransformation(transformMatrix, transformVector);
| ^
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function ‘virtual void gmx::test::AffineTransformationTest_identityTransformYieldsSameVectors_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:199:93: note: parameter passing for argument of type ‘gmx::Matrix3x3ConstSpan’ {aka ‘gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >’} changed in GCC 7.1
199 | const AffineTransformation identityTransformation(identityMatrix<real, 3>(), { 0, 0, 0 });
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp: In function ‘void gmx::test::pmeInitAtoms(gmx_pme_t*, gmx::StatePropagatorDataGpu*, gmx::test::CodePath, const CoordinatesVector&, const ChargesVector&)’:
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp:202:43: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
202 | stateGpu->copyCoordinatesToGpu(arrayRefFromArray(coordinates.data(), coordinates.size()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
203 | gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function ‘virtual void gmx::test::TranslateAndScaleTest_identityTransformation_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:91:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
91 | translateAndScale(toBeTransformed);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function ‘virtual void gmx::test::TranslateAndScaleTest_translationWithIdentityScaling_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:98:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
98 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function ‘virtual void gmx::test::TranslateAndScaleTest_scalingWithZeroTranslation_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:108:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
108 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function ‘virtual void gmx::test::TranslateAndScaleTest_translationAndScalingNonTrivial_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:118:22: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
118 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function ‘virtual void gmx::test::TranslateAndScaleTest_scalingIdentity_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:140:10: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
140 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function ‘virtual void gmx::test::TranslateAndScaleTest_scalingNonTrivial_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:150:10: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
150 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function ‘virtual void gmx::test::TranslateAndScaleTest_scalingInverseNoZero_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:170:10: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
170 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:171:35: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
171 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function ‘virtual void gmx::test::TranslateAndScaleTest_scalingInverseWithOneScaleDimensionZero_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:179:10: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
179 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:180:35: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
180 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/device_buffer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/typecasts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/template_mp.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
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Scanning dependencies of target mdrunutility-test-shared
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdspan-test
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1
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[ 73%] Built target mdrunutility-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
/usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdtypes-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests/checkpointdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/listoflists.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mdmodulenotification-impl.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/range.cpp.o CMakeFiles/utility-test.dir/strconvert.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/template_mp.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target utility-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/tests/forcebuffers.cpp
[ 75%] Built target mdspan-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target onlinehelp-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/neldermead.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target mdtypes-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/optimization.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/optimization.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/neldermead.cpp: In static member function ‘static real gmx::test::{anonymous}::NelderMeadSimplexTest::doubleFirstCoordinateValue(gmx::ArrayRef<const double>)’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/neldermead.cpp:75:17: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
75 | static real doubleFirstCoordinateValue(ArrayRef<const real> x) { return 2 * x[0]; }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/optimization.cpp: In function ‘real gmx::test::{anonymous}::mcCormick(gmx::ArrayRef<const double>)’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/optimization.cpp:61:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
61 | real mcCormick(ArrayRef<const real> x)
| ^~~~~~~~~
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp: In member function ‘virtual void gmx::test::{anonymous}::MatrixTest_transposeWorks_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp:174:70: note: parameter passing for argument of type ‘gmx::Matrix3x3ConstSpan’ {aka ‘gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >’} changed in GCC 7.1
174 | const Matrix3x3 transposedAsymmetricMat = transpose(asymmetricMat);
| ^
/<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp: In member function ‘virtual void gmx::test::{anonymous}::MatrixTest_transposeOfSymmetricMatrix_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp:189:68: note: parameter passing for argument of type ‘gmx::Matrix3x3ConstSpan’ {aka ‘gmx::basic_mdspan<const double, gmx::extents<3, 3>, gmx::layout_right, gmx::accessor_basic<const double> >’} changed in GCC 7.1
189 | const Matrix3x3 transposedSymmetricMat = transpose(symmetricMat);
| ^
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pbcutil-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp: In member function ‘virtual void gmx::test::{anonymous}::COMInPlaceTest_MatrixDefault_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp:168:33: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
168 | placeCoordinatesWithCOMInBox(pbcType, unitcell, center, box, testCoordinates_, testTopology_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 | COMShiftType::Molecule);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp:182:33: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
182 | placeCoordinatesWithCOMInBox(pbcType, unitcell, center, box, testCoordinates_, testTopology_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | COMShiftType::Residue);
| ~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/pbcutil/com.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp:44:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<gmx::BasicVector<double> > gmx::test::{anonymous}::initialCoordinates()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp: In member function ‘virtual void gmx::test::{anonymous}::ShiftTest_CoordinateShiftWorks_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/com.cpp:195:15: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
195 | shiftAtoms(shift, coords);
| ~~~~~~~~~~^~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/mshift.cpp:44:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<gmx::BasicVector<double> > gmx::test::{anonymous}::coordinates()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<gmx::BasicVector<double> > gmx::test::{anonymous}::coordinatesWhole()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp:48:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::RVecTest_ConvertsImplicitlyTo_rvec_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::RVecTest_WorksAsMutable_rvec_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::RVecTest_CanBeStoredInVector_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::RVecTest_WorksAs_rvec_Array_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/com.cpp.o CMakeFiles/pbcutil-test.dir/mshift.cpp.o CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target pbcutil-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/random/uniformrealdistribution.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/random/exponentialdistribution.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ExponentialDistributionTest_Output_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/random/uniformrealdistribution.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/random/exponentialdistribution.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/gammadistribution.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = const double]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::GammaDistributionTest_Output_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘std::enable_if_t<is_same_v<typename std::remove_const<_Tp>::type, typename std::remove_const<U>::type>, void> gmx::test::compareViewsIgnoreConst(gmx::ArrayRef<T>, gmx::ArrayRef<U>) [with T = double; U = const double]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
100 | compareViewsIgnoreConst(ArrayRef<T> input, ArrayRef<U> output)
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
111 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:111:6: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘std::enable_if_t<is_same_v<typename std::remove_const<_Tp>::type, typename std::remove_const<U>::type>, void> gmx::test::compareViewsIgnoreConst(gmx::ArrayRef<T>, gmx::ArrayRef<U>) [with T = gmx::BasicVector<double>; U = const gmx::BasicVector<double>]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
100 | compareViewsIgnoreConst(ArrayRef<T> input, ArrayRef<U> output)
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:100:1: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function ‘void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = const gmx::BasicVector<double>]’:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
88 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:88:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/random/uniformrealdistribution.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/random/normaldistribution.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::NormalDistributionTest_Output_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::test::resizeAndFillInput(PaddedVectorOfT*, int, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]’:
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/bits/random.h:34,
from /usr/include/c++/11/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]’:
/usr/include/c++/11/bits/stl_vector.h:625:7: note: parameter passing for argument of type ‘std::initializer_list<long long unsigned int>’ changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/bits/random.h:34,
from /usr/include/c++/11/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ThreeFry2x64Test_InternalCounterSequence_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ThreeFry2x64Test_Fast_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ThreeFry2x64Test_Default_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::ThreeFry2x64Test_Using40Rounds_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’:
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type ‘std::initializer_list<long long unsigned int>’ changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type ‘std::initializer_list<long long unsigned int>’ changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type ‘std::initializer_list<long long unsigned int>’ changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 77%] Built target options-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/neldermead.cpp.o CMakeFiles/math-test.dir/optimization.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 79%] Built target math-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function ‘void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]’:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/random/uniformrealdistribution.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::UniformRealDistributionTest_GenerateCanonical_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::UniformRealDistributionTest_Output_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 80%] Built target random-test
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target topology-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function ‘void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]’:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function ‘void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]’:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function ‘void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]’:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:46:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type ‘std::initializer_list<gmx::NumericalSplineTableInput>’ changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:192:5: note: in expansion of macro ‘GMX_TEST_THROW_’
192 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro ‘EXPECT_THROW_GMX’
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/topology-test.dir/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/idef.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 80%] Built target pull-test
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 80%] Built target taskassignment-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target table-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/mp11.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/mp11.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxana-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/idef.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target topology-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/math/vec.h:111,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void gmx::{anonymous}::Entropy::runQuasiHarmonic(real, gmx_bool)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In function ‘void gmx::{anonymous}::Entropy::runSchlitter(real, gmx_bool)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx3-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx2-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 83%] Built target pdb2gmx3-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target gmxana-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx1-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target pdb2gmx2-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target simd-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
Scanning dependencies of target correlations-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test-shared
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genrestr.cpp
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[ 85%] Built target pdb2gmx1-test
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target coordinateio-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp:46:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::AutocorrTest_EacP1_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::AutocorrTest_EacCos_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::AutocorrTest_EacNormal_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::AutocorrTest_EacP4_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::AutocorrTest_EacNoNormalize_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::AutocorrTest_EacP2_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::AutocorrTest_EacP3_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::AutocorrTest_EacVector_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::AutocorrTest_EacRcross_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void gmx::{anonymous}::AutocorrTest_EacP0_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValueAndError(int, int, real, real)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real, real)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::test::AnalysisDataTestInputFrame}; _Tp = gmx::test::AnalysisDataTestInputFrame; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputFrame>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::test::AnalysisDataTestInputFrame>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘gmx::test::AnalysisDataTestInputFrame& gmx::test::AnalysisDataTestInput::addFrame(real)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputFrame*, std::vector<gmx::test::AnalysisDataTestInputFrame> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real, real)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void gmx::test::AnalysisDataTestInput::addFrameWithValueAndError(real, real, real)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFromTypeNumber_Test]’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddTypeWorks_Test]’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_WrongNameNotFound_Test]’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_EmptyOnCreate_Test]’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_IndexOutOfRangeInvalid_Test]’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CannotAddDuplicateEntry_Test]’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFound_Test]’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddMultipleTypesWorks_Test]’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function ‘testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_NoNameFromIncorrectTypeNumber_Test]’:
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:36: note: parameter passing for argument of type ‘gmx::ArrayRef<const double>’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp:51:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In static member function ‘static void gmx::{anonymous}::ExpfitTest::SetUpTestCase()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target analysisdata-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target gmxpreprocess-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target energyanalysis-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/checkpoint.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target coordinateio-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/helpwriting.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp:44:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
/usr/include/c++/11/bits/vector.tcc: In member function ‘testing::Test* testing::internal::ParameterizedTestFactory<TestClass>::CreateTest() [with TestClass = {anonymous}::StructureIORoundtripTest_ReadWriteTpsConf_Test]’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-modules-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp: In member function ‘virtual void gmx::test::{anonymous}::MrcDensityMap_ReadsCoordinateTransformationFromFile_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:110:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
110 | coordinateTransformation({ &coordinate1, &coordinate1 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:111:29: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
111 | coordinateTransformation({ &coordinate2, &coordinate2 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const {anonymous}::NeighborhoodSearchTestData::RefPair&}; _Tp = {anonymous}::NeighborhoodSearchTestData::RefPair; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::RefPair>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function ‘virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformNoOriginGiven_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:89:49: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
89 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function ‘virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithOriginDefined_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:108:49: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
108 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void {anonymous}::NeighborhoodSearchTestData::computeReferencesInternal(t_pbc*, bool)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double*&}; _Tp = {anonymous}::NeighborhoodSearchTestData::TestPosition; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::TestPosition>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function ‘virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithStartValues_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:126:49: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
126 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
/usr/include/c++/11/bits/vector.tcc: In member function ‘void {anonymous}::NeighborhoodSearchTestData::useRefPositionsAsTestPositions()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In static member function ‘static void {anonymous}::NeighborhoodSearchTest::testPairSearch(gmx::AnalysisNeighborhoodSearch*, const {anonymous}::NeighborhoodSearchTestData&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::BasicVector<double>}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘void {anonymous}::NeighborhoodSearchTestData::generateRandomRefPositions(int)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In static member function ‘static const {anonymous}::NeighborhoodSearchTestData& {anonymous}::RandomBoxXYFullPBCData::get()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/vector.tcc: In static member function ‘static const {anonymous}::NeighborhoodSearchTestData& {anonymous}::TrivialTestData::get()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::NeighborhoodSearchTest_HandlesConcurrentSearches_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::NeighborhoodSearchTest_HandlesSkippingPairs_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::NeighborhoodSearchTest_SimpleSelfPairsSearch_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::NeighborhoodSearchTest_HandlesNoPBC_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In static member function ‘static const {anonymous}::NeighborhoodSearchTestData& {anonymous}::RandomBoxFullPBCData::get()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearchExclusions_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::NeighborhoodSearchTest_GridSearchExclusions_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void {anonymous}::NeighborhoodSearchTest_GridSelfPairsSearch_Test::TestBody()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::NeighborhoodSearchTest_GridSearchTriclinic_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::NeighborhoodSearchTest_GridSearch2DPBC_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:50:
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::NeighborhoodSearchTest_GridSearchNoPBC_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::NeighborhoodSearchTest_HandlesNullPBC_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/11/bits/vector.tcc: In static member function ‘static void {anonymous}::NeighborhoodSearchTest::testPairSearchIndexed(gmx::AnalysisNeighborhood*, const {anonymous}::NeighborhoodSearchTestData&, uint64_t)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target mdrun-modules-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-pme-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pme-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In static member function ‘static void gmx::test::XvgioTest::compareValues(gmx::basic_mdspan<const double, gmx::extents<-1, -1> >, gmx::basic_mdspan<const double, gmx::extents<-1, -1> >)’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:75:17: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
75 | static void compareValues(basic_mdspan<const double, dynamicExtents2D> ref,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:75:17: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function ‘virtual void gmx::test::XvgioTest_readXvgIgnoreCommentLineWorks_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:150:18: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
150 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:150:18: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function ‘virtual void gmx::test::XvgioTest_readXvgRealWorks_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:132:18: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
132 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:132:18: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp: In member function ‘virtual void gmx::test::XvgioTest_readXvgIntWorks_Test::TestBody()’:
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:113:18: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
113 | compareValues(xvgRefData.asConstView(), xvgTestData.asConstView());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/xvgio.cpp:113:18: note: parameter passing for argument of type ‘gmx::basic_mdspan<const double, gmx::extents<-1, -1> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/checkpoint.cpp.o CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/xvgio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pme-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-pme-test.dir/pmetest.cpp.o CMakeFiles/mdrun-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target fileio-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target mdrun-pme-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-io-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 90%] Built target mdrun-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/ewaldsurfaceterm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target selection-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
Scanning dependencies of target mdrun-mpi-coordination-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multiple_time_stepping.cpp
Scanning dependencies of target mdrun-simulator-comparison-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-output-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 92%] Built target mdrun-mpi-coordination-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 92%] Built target mdrun-simulator-comparison-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/ewaldsurfaceterm.cpp.o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-tpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-output-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-tpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-pme-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrunfep-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunfep-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/freeenergy.cpp
Scanning dependencies of target nblib-integrator-test
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cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp
Scanning dependencies of target nblib-setup-test
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cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/box.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target mdrun-mpi-pme-test
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/particletype.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake --color=
Scanning dependencies of target nblib-integration-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_IntegratorWorks_Test::TestBody()’:
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp:124:33: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
124 | integrator.integrate(dt, simulationState.coordinates(), simulationState.velocities(),
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
125 | simulationState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp:124:33: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp:124:33: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/integrator.cpp:124:33: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/pbcholder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp:44:
/<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_GmxForceCalculatorCanCompute_Test::TestBody()’:
/<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp:66:48: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
66 | EXPECT_NO_THROW(gmxForceCalculator->compute(simState.coordinates(), simState.forces()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp:66:48: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/gmxcalculator.cpp:66:48: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunfep-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunfep-test.dir/freeenergy.cpp.o CMakeFiles/mdrunfep-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrunfep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target nblib-integrator-test
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target mdrunfep-test
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/nbnxnsetup.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:45:
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_SpcMethanolForcesAreCorrect_Test::TestBody()’:
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:82:44: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
82 | ASSERT_NO_THROW(forceCalculator.compute(simState.coordinates(), forces));
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:82:44: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:82:44: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_CanIntegrateSystem_Test::TestBody()’:
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:119:32: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
119 | forceCalculator.compute(simState.coordinates(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:119:32: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:119:32: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:45:
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:120:45: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
120 | EXPECT_NO_THROW(integrator.integrate(1.0, simState.coordinates(), simState.velocities(),
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
121 | simState.forces()));
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:120:45: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:120:45: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:120:45: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_ArgonForcesAreCorrect_Test::TestBody()’:
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:207:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
207 | forceCalculator.compute(simState.coordinates(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:207:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:207:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_ExpectedNumberOfForces_Test::TestBody()’:
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:99:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
99 | forceCalculator.compute(simState.coordinates(), forces);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:99:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:99:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_UpdateChangesForces_Test::TestBody()’:
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:153:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
153 | forceCalculator.compute(simState.coordinates(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:153:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:153:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:163:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
163 | forceCalculator.compute(simState.coordinates(), forces);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:163:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:163:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:175:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
175 | integrator.integrate(1.0, simState.coordinates(), simState.velocities(), simState.forces());
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:175:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:175:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:175:25: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:181:28: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
181 | forceCalculator.compute(simState.coordinates(), forces);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:181:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/tests/nbkernelsystem.cpp:181:28: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target nblib-listed-forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/bondtypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/tests/simstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/helpers.cpp
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Distance = int; _Tp = std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/kernels.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o CMakeFiles/nblib-integration-test.dir/nbnxnsetup.cpp.o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target nblib-integration-test
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nblib::StrongType<double, nblib::MassParameter>}; _Tp = nblib::StrongType<double, nblib::MassParameter>; _Alloc = std::allocator<nblib::StrongType<double, nblib::MassParameter> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::StrongType<double, nblib::MassParameter> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::collectInteractions(const std::vector<std::tuple<nblib::Molecule, int> >&) [with I = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::ParticleType&}; _Tp = nblib::ParticleType; _Alloc = std::allocator<nblib::ParticleType>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::ParticleType>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_TopologyHasParticleTypeIds_Test::TestBody()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::ParticleType*, std::vector<nblib::ParticleType> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:60,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-internal.h:58,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:47,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<std::tuple<int, int>&&>, std::tuple<>}; _Key = std::tuple<int, int>; _Val = std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >; _KeyOfValue = std::_Select1st<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >; _Compare = std::less<std::tuple<int, int> >; _Alloc = std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >]’:
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::tuple<int, int>, std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >, std::_Select1st<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >, std::less<std::tuple<int, int> >, std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >::const_iterator’ changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-internal.h:58,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:59,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:47,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/11/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = std::tuple<int, int>; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Compare = std::less<std::tuple<int, int> >; _Alloc = std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >]’:
/usr/include/c++/11/bits/stl_map.h:520:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::tuple<int, int>, std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >, std::_Select1st<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >, std::less<std::tuple<int, int> >, std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >::const_iterator’ changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_TopologyListedInteractions_Test::TestBody()’:
/usr/include/c++/11/bits/stl_map.h:520:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::tuple<int, int>, std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >, std::_Select1st<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >, std::less<std::tuple<int, int> >, std::allocator<std::pair<const std::tuple<int, int>, nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >::const_iterator’ changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_TopologyHasMasses_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::StrongType<double, nblib::MassParameter>*, std::vector<nblib::StrongType<double, nblib::MassParameter> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_TopologyCanAggregateBonds_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1642 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib/util/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake --color=
Scanning dependencies of target nblib-util-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/tests/setup.cpp
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp:53,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp:44:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/stl_vector.h:625:7: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<nblib::detail::eliminateDuplicateInteractions<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >(const std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >&)::<lambda(const auto:24&, const auto:25&)> >]’:
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘std::tuple<std::vector<unsigned int, std::allocator<unsigned int> >, std::vector<T, std::allocator<_Tp1> > > nblib::detail::eliminateDuplicateInteractions(const std::vector<T>&) [with I = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>]’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>*, std::vector<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int>, std::allocator<std::tuple<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, unsigned int> > > >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:43,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/api/nblib/tests/topology.cpp:44:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’:
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp:56:37: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
56 | std::vector<std::vector<gmx::RVec>> c_coordinatesForTests = {
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp:56:37: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/typetests.cpp:56:37: note: parameter passing for argument of type ‘std::initializer_list<gmx::BasicVector<double> >’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/api/nblib/util/tests/setup.cpp:44:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:54:
/<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp: In function ‘auto nblib::computeForces(const std::vector<T>&, const std::vector<TwoCenterType>&, gmx::ArrayRef<const gmx::BasicVector<double> >, Buffer*, const Pbc&) [with Index = std::array<int, 3>; InteractionType = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; Buffer = std::vector<gmx::BasicVector<double> >; Pbc = nblib::PbcHolder]’:
/<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp:392:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
392 | auto computeForces(const std::vector<Index>& indices,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_isRealValued_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {float, float, float}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_checkNumericValuesHasNan_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp: In function ‘auto nblib::computeForces(const std::vector<T>&, const std::vector<TwoCenterType>&, gmx::ArrayRef<const gmx::BasicVector<double> >, Buffer*, const Pbc&) [with Index = std::array<int, 4>; InteractionType = nblib::HarmonicAngleType; Buffer = std::vector<gmx::BasicVector<double> >; Pbc = nblib::PbcHolder]’:
/<<PKGBUILDDIR>>/api/nblib/listed_forces/dataflow.hpp:392:6: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void nblib::test::{anonymous}::NBlibTest_checkNumericValuesHasInf_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/util/tests/traits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /usr/include/c++/11/valarray:38,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:49:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>&}; _Tp = nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>; _Alloc = std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp: In member function ‘virtual void nblib::test::{anonymous}::LinearChainDataFixture_Multithreading_Test::TestBody()’:
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:234:25: note: parameter passing for argument of type ‘gmx::ArrayRef<const gmx::BasicVector<double> >’ changed in GCC 7.1
234 | lfCalculator.compute(x, forces, energies);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:234:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
/<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:234:25: note: parameter passing for argument of type ‘gmx::ArrayRef<gmx::BasicVector<double> >’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /usr/include/c++/11/valarray:38,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/calculator.cpp:49:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘nblib::LinearChainData::LinearChainData(int, float)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>*, std::vector<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter>, std::allocator<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-setup-test.dir/box.cpp.o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o CMakeFiles/nblib-setup-test.dir/topology.cpp.o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so ../../../lib/libgtest.so -lpthread ../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/conversions.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target nblib-setup-test
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/transformations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/api -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/nblib-util-test.dir/setup.cpp.o CMakeFiles/nblib-util-test.dir/traits.cpp.o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
[ 96%] Built target nblib-util-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
Scanning dependencies of target commandline-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/conversions.cpp:46:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<t_iparams>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:57,
from /<<PKGBUILDDIR>>/api/nblib/listed_forces/tests/conversions.cpp:46:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void nblib::detail::transferParameters(const InteractionData&, gmx_ffparams_t&) [with InteractionData = nblib::ListedTypeData<nblib::ProperDihedral>]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In function ‘void nblib::detail::transferParameters(const InteractionData&, gmx_ffparams_t&) [with InteractionData = nblib::ListedTypeData<nblib::TwoParameterInteraction<nblib::HarmonicBondTypeParameter> >]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In function ‘void nblib::detail::transferParameters(const InteractionData&, gmx_ffparams_t&) [with InteractionData = nblib::ListedTypeData<nblib::HarmonicAngleType>]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In function ‘std::tuple<std::unique_ptr<InteractionDefinitions, std::default_delete<InteractionDefinitions> >, std::unique_ptr<gmx_ffparams_t, std::default_delete<gmx_ffparams_t> > > nblib::createFFparams(const ListedInteractionData&)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/api/nblib /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/api/nblib /<<PKGBUILDDIR>>/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake --color=
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make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target nblib-tests
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gmx::BasicVector<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘void {anonymous}::SurfaceAreaTest::generateRandomPositions(int)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::SurfaceAreaTest_ComputesSinglePoint_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPoints_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPointsOfUnequalRadius_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::SurfaceAreaTest_SurfacePoints12_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::SurfaceAreaTest_SurfacePoints32_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/g++-11 -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::SurfaceAreaTest_SurfacePoints42_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/vector.tcc: In member function ‘virtual void {anonymous}::SurfaceAreaTest_SurfacePoints122_Test::TestBody()’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:45:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/g++-11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.6.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/11/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
(cd build/basic-dp; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic-dp
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: NbLibListedForcesTests
1: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml"
1: Test timeout computed to be: 600
1: [==========] Running 23 tests from 9 test cases.
1: [----------] Global test environment set-up.
1: [----------] 5 tests from NBlibTest
1: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks
1: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms)
1: [ RUN ] NBlibTest.BondTypesLessThanWorks
1: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms)
1: [ RUN ] NBlibTest.CanSplitListedWork
1: [ OK ] NBlibTest.CanSplitListedWork (0 ms)
1: [ RUN ] NBlibTest.ListedForceBuffer
1: [ OK ] NBlibTest.ListedForceBuffer (0 ms)
1: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct
1: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (1 ms)
1: [----------] 5 tests from NBlibTest (1 ms total)
1:
1: [----------] 1 test from Kernels
1: [ RUN ] Kernels.HarmonicScalarKernelCanCompute
1: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms)
1: [----------] 1 test from Kernels (0 ms total)
1:
1: [----------] 5 tests from ListedExampleData
1: [ RUN ] ListedExampleData.ComputeHarmonicBondForces
1: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms)
1: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies
1: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms)
1: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces
1: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (1 ms)
1: [ RUN ] ListedExampleData.CanReduceForces
1: [ OK ] ListedExampleData.CanReduceForces (0 ms)
1: [ RUN ] ListedExampleData.CanReduceEnergies
1: [ OK ] ListedExampleData.CanReduceEnergies (0 ms)
1: [----------] 5 tests from ListedExampleData (1 ms total)
1:
1: [----------] 1 test from LinearChainDataFixture
1: [ RUN ] LinearChainDataFixture.Multithreading
1: [ OK ] LinearChainDataFixture.Multithreading (3 ms)
1: [----------] 1 test from LinearChainDataFixture (3 ms total)
1:
1: [----------] 1 test from ListedShims
1: [ RUN ] ListedShims.ParameterConversion
1: [ OK ] ListedShims.ParameterConversion (0 ms)
1: [----------] 1 test from ListedShims (0 ms total)
1:
1: [----------] 1 test from ListedTransformations
1: [ RUN ] ListedTransformations.SortInteractionIndices
1: [ OK ] ListedTransformations.SortInteractionIndices (0 ms)
1: [----------] 1 test from ListedTransformations (0 ms total)
1:
1: [----------] 3 tests from FourCenter/ProperDihedralTest
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/0
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/0 (0 ms)
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/1
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/1 (1 ms)
1: [ RUN ] FourCenter/ProperDihedralTest.CheckListed/2
1: [ OK ] FourCenter/ProperDihedralTest.CheckListed/2 (0 ms)
1: [----------] 3 tests from FourCenter/ProperDihedralTest (1 ms total)
1:
1: [----------] 3 tests from TwoCenter/HarmonicBondTest
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/0
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/0 (0 ms)
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/1
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/1 (1 ms)
1: [ RUN ] TwoCenter/HarmonicBondTest.CheckListed/2
1: [ OK ] TwoCenter/HarmonicBondTest.CheckListed/2 (0 ms)
1: [----------] 3 tests from TwoCenter/HarmonicBondTest (1 ms total)
1:
1: [----------] 3 tests from ThreeCenter/HarmonicAngleTest
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/0
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/0 (1 ms)
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/1
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/1 (0 ms)
1: [ RUN ] ThreeCenter/HarmonicAngleTest.CheckListed/2
1: [ OK ] ThreeCenter/HarmonicAngleTest.CheckListed/2 (0 ms)
1: [----------] 3 tests from ThreeCenter/HarmonicAngleTest (1 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 23 tests from 9 test cases ran. (8 ms total)
1: [ PASSED ] 23 tests.
1/65 Test #1: NbLibListedForcesTests ................ Passed 1.24 sec
test 2
Start 2: NbLibSamplesTestArgon
2: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/argon-forces-integration
2: Test timeout computed to be: 1500
2: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000
2: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189
2: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000
2: final position of particle 0: x 0.789162 y 1.271508 z 0.819867
2/65 Test #2: NbLibSamplesTestArgon ................. Passed 0.10 sec
test 3
Start 3: NbLibSamplesTestMethaneWater
3: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/methane-water-integration
3: Test timeout computed to be: 1500
3: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000
3: final position of particle 9: x 0.151648 y 4.370903 z 5.083184
3/65 Test #3: NbLibSamplesTestMethaneWater .......... Passed 0.07 sec
test 4
Start 4: NbLibUtilTests
4: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 16 tests from 2 test cases.
4: [----------] Global test environment set-up.
4: [----------] 6 tests from NBlibTest
4: [ RUN ] NBlibTest.isRealValued
4: [ OK ] NBlibTest.isRealValued (0 ms)
4: [ RUN ] NBlibTest.checkNumericValuesHasNan
4: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms)
4: [ RUN ] NBlibTest.checkNumericValuesHasInf
4: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms)
4: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (1 ms)
4: [ RUN ] NBlibTest.generateVelocitySize
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.generateVelocitySize (0 ms)
4: [ RUN ] NBlibTest.generateVelocityCheckNumbers
4: Velocities were taken from a Maxwell distribution at 300 K
4: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms)
4: [----------] 6 tests from NBlibTest (1 ms total)
4:
4: [----------] 10 tests from NblibTraitsUtils
4: [ RUN ] NblibTraitsUtils.FuseTwo
4: [ OK ] NblibTraitsUtils.FuseTwo (0 ms)
4: [ RUN ] NblibTraitsUtils.Fuse
4: [ OK ] NblibTraitsUtils.Fuse (0 ms)
4: [ RUN ] NblibTraitsUtils.Repeat
4: [ OK ] NblibTraitsUtils.Repeat (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTuple1
4: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTuple2
4: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeList1
4: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeList2
4: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms)
4: [ RUN ] NblibTraitsUtils.Contains
4: [ OK ] NblibTraitsUtils.Contains (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated
4: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms)
4: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated
4: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms)
4: [----------] 10 tests from NblibTraitsUtils (0 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 16 tests from 2 test cases ran. (1 ms total)
4: [ PASSED ] 16 tests.
4/65 Test #4: NbLibUtilTests ........................ Passed 0.05 sec
test 5
Start 5: NbLibSetupTests
5: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml"
5: Test timeout computed to be: 600
5: [==========] Running 39 tests from 1 test case.
5: [----------] Global test environment set-up.
5: [----------] 39 tests from NBlibTest
5: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN
5: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms)
5: [ RUN ] NBlibTest.CubicBoxCannotHaveInf
5: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms)
5: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN
5: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms)
5: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf
5: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms)
5: [ RUN ] NBlibTest.CubicBoxWorks
5: [ OK ] NBlibTest.CubicBoxWorks (0 ms)
5: [ RUN ] NBlibTest.NonBondedForceParamsCorrect
5: [ OK ] NBlibTest.NonBondedForceParamsCorrect (1 ms)
5: [ RUN ] NBlibTest.CanMergeInteractions
5: [ OK ] NBlibTest.CanMergeInteractions (0 ms)
5: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed
5: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms)
5: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed
5: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms)
5: [ RUN ] NBlibTest.PbcHolderWorks
5: [ OK ] NBlibTest.PbcHolderWorks (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms)
5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName
5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms)
5: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule
5: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms)
5: [ RUN ] NBlibTest.CanConstructExclusionListFromNames
5: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms)
5: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed
5: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms)
5: [ RUN ] NBlibTest.AtWorks
5: [ OK ] NBlibTest.AtWorks (0 ms)
5: [ RUN ] NBlibTest.AtThrows
5: [ OK ] NBlibTest.AtThrows (0 ms)
5: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass
5: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms)
5: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass
5: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms)
5: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName
5: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms)
5: [ RUN ] NBlibTest.CanAddInteractions
5: [ OK ] NBlibTest.CanAddInteractions (0 ms)
5: [ RUN ] NBlibTest.TopologyHasNumParticles
5: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms)
5: [ RUN ] NBlibTest.TopologyHasCharges
5: [ OK ] NBlibTest.TopologyHasCharges (1 ms)
5: [ RUN ] NBlibTest.TopologyHasMasses
5: [ OK ] NBlibTest.TopologyHasMasses (0 ms)
5: [ RUN ] NBlibTest.TopologyHasParticleTypes
5: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms)
5: [ RUN ] NBlibTest.TopologyHasParticleTypeIds
5: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms)
5: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType
5: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms)
5: [ RUN ] NBlibTest.TopologyHasExclusions
5: [ OK ] NBlibTest.TopologyHasExclusions (1 ms)
5: [ RUN ] NBlibTest.TopologyHasSequencing
5: [ OK ] NBlibTest.TopologyHasSequencing (0 ms)
5: [ RUN ] NBlibTest.TopologyCanAggregateBonds
5: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms)
5: [ RUN ] NBlibTest.TopologyCanSequencePairIDs
5: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms)
5: [ RUN ] NBlibTest.TopologySequenceIdThrows
5: No particle O-Atom in residue SOL in molecule SOL found
5: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms)
5: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds
5: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms)
5: [ RUN ] NBlibTest.TopologyListedInteractions
5: [ OK ] NBlibTest.TopologyListedInteractions (0 ms)
5: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes
5: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms)
5: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows
5: No particle Iron in residue SOL in molecule SOL found
5: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (1 ms)
5: [ RUN ] NBlibTest.toGmxExclusionBlockWorks
5: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms)
5: [----------] 39 tests from NBlibTest (6 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 39 tests from 1 test case ran. (6 ms total)
5: [ PASSED ] 39 tests.
5/65 Test #5: NbLibSetupTests ....................... Passed 0.04 sec
test 6
Start 6: NbLibIntegrationTests
6: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml"
6: Test timeout computed to be: 600
6: [==========] Running 19 tests from 1 test case.
6: [----------] Global test environment set-up.
6: [----------] 19 tests from NBlibTest
6: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute
6: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (2 ms)
6: [ RUN ] NBlibTest.CanSetupStepWorkload
6: [ OK ] NBlibTest.CanSetupStepWorkload (0 ms)
6: [ RUN ] NBlibTest.GmxForceCalculatorCanSetupInteractionConst
6: [ OK ] NBlibTest.GmxForceCalculatorCanSetupInteractionConst (1 ms)
6: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect
6: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (1 ms)
6: [ RUN ] NBlibTest.ExpectedNumberOfForces
6: [ OK ] NBlibTest.ExpectedNumberOfForces (2 ms)
6: [ RUN ] NBlibTest.CanIntegrateSystem
6: [ OK ] NBlibTest.CanIntegrateSystem (1 ms)
6: [ RUN ] NBlibTest.UpdateChangesForces
6: [ OK ] NBlibTest.UpdateChangesForces (1 ms)
6: [ RUN ] NBlibTest.ArgonForcesAreCorrect
6: [ OK ] NBlibTest.ArgonForcesAreCorrect (1 ms)
6: [ RUN ] NBlibTest.CanConstructNbvSetupUtil
6: [ OK ] NBlibTest.CanConstructNbvSetupUtil (0 ms)
6: [ RUN ] NBlibTest.CanConstructSimulationState
6: [ OK ] NBlibTest.CanConstructSimulationState (1 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN
6: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF
6: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN
6: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (1 ms)
6: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF
6: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms)
6: [ RUN ] NBlibTest.SimulationStateCanMove
6: [ OK ] NBlibTest.SimulationStateCanMove (0 ms)
6: [ RUN ] NBlibTest.SimulationStateCanAssign
6: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasBox
6: [ OK ] NBlibTest.SimulationStateHasBox (1 ms)
6: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates
6: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms)
6: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities
6: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms)
6: [----------] 19 tests from NBlibTest (12 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 19 tests from 1 test case ran. (12 ms total)
6: [ PASSED ] 19 tests.
6/65 Test #6: NbLibIntegrationTests ................. Passed 0.04 sec
test 7
Start 7: NbLibIntegratorTests
7: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml"
7: Test timeout computed to be: 600
7: [==========] Running 1 test from 1 test case.
7: [----------] Global test environment set-up.
7: [----------] 1 test from NBlibTest
7: [ RUN ] NBlibTest.IntegratorWorks
7: [ OK ] NBlibTest.IntegratorWorks (1 ms)
7: [----------] 1 test from NBlibTest (1 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 1 test from 1 test case ran. (1 ms total)
7: [ PASSED ] 1 test.
7/65 Test #7: NbLibIntegratorTests .................. Passed 0.04 sec
test 8
Start 8: TestUtilsUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 59 tests from 5 test cases.
8: [----------] Global test environment set-up.
8: [----------] 10 tests from InteractiveTestHelperTest
8: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
8: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (2 ms)
8: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
8: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
8: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
8: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
8: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms)
8: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
8: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms)
8: [----------] 10 tests from InteractiveTestHelperTest (13 ms total)
8:
8: [----------] 34 tests from ReferenceDataTest
8: [ RUN ] ReferenceDataTest.HandlesSimpleData
8: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
8: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
8: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesStringBlockData
8: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesVectorData
8: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceData
8: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
8: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesIncorrectData
8: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
8: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMissingData
8: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedData
8: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
8: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
8: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnys
8: [ OK ] ReferenceDataTest.HandlesAnys (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
8: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
8: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
8: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
8: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
8: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
8: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
8: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
8: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
8: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
8: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
8: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
8: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
8: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
8: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesReadingValues
8: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms)
8: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
8: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
8: [----------] 34 tests from ReferenceDataTest (22 ms total)
8:
8: [----------] 7 tests from FloatingPointDifferenceTest
8: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
8: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
8: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
8: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
8: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
8: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
8: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
8: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
8: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
8: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
8:
8: [----------] 4 tests from FloatingPointToleranceTest
8: [ RUN ] FloatingPointToleranceTest.UlpTolerance
8: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
8: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
8: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
8: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
8: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
8: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
8: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
8: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
8:
8: [----------] 4 tests from XvgTests
8: [ RUN ] XvgTests.CreateFile
8: [ OK ] XvgTests.CreateFile (1 ms)
8: [ RUN ] XvgTests.CheckMissing
8: [ OK ] XvgTests.CheckMissing (0 ms)
8: [ RUN ] XvgTests.CheckExtra
8: [ OK ] XvgTests.CheckExtra (0 ms)
8: [ RUN ] XvgTests.ReadIncorrect
8: [ OK ] XvgTests.ReadIncorrect (1 ms)
8: [----------] 4 tests from XvgTests (4 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 59 tests from 5 test cases ran. (41 ms total)
8: [ PASSED ] 59 tests.
8/65 Test #8: TestUtilsUnitTests .................... Passed 0.08 sec
test 9
Start 9: TestUtilsMpiUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 1 test from 1 test case.
9: [----------] Global test environment set-up.
9: [----------] 1 test from MpiSelfTest
9: [ RUN ] MpiSelfTest.Runs
9: [ OK ] MpiSelfTest.Runs (1 ms)
9: [----------] 1 test from MpiSelfTest (1 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 1 test from 1 test case ran. (1 ms total)
9: [ PASSED ] 1 test.
9/65 Test #9: TestUtilsMpiUnitTests ................. Passed 0.03 sec
test 10
Start 10: UtilityUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 373 tests from 61 test cases.
10: [----------] Global test environment set-up.
10: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.Move
10: [ OK ] AllocatorTest/0.Move (0 ms)
10: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/0 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<double, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.Move
10: [ OK ] AllocatorTest/1.Move (0 ms)
10: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/1 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.Move
10: [ OK ] AllocatorTest/2.Move (0 ms)
10: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/2 (0 ms total)
10:
10: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.Move
10: [ OK ] AllocatorTest/3.Move (0 ms)
10: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/3 (1 ms total)
10:
10: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (2 ms)
10: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/4.Move
10: [ OK ] AllocatorTest/4.Move (0 ms)
10: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/4 (2 ms total)
10:
10: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::PageAlignedAllocationPolicy>
10: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/5.Move
10: [ OK ] AllocatorTest/5.Move (0 ms)
10: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
10: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
10: [----------] 5 tests from AllocatorTest/5 (2 ms total)
10:
10: [----------] 1 test from AllocatorUntypedTest
10: [ RUN ] AllocatorUntypedTest.Comparison
10: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
10: [----------] 1 test from AllocatorUntypedTest (0 ms total)
10:
10: [----------] 1 test from EmptyArrayRefTest
10: [ RUN ] EmptyArrayRefTest.IsEmpty
10: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
10: [----------] 1 test from EmptyArrayRefTest (0 ms total)
10:
10: [----------] 1 test from EmptyConstArrayRefTest
10: [ RUN ] EmptyConstArrayRefTest.IsEmpty
10: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
10: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
10: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/0 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
10: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/1 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
10: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/2 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
10: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/3 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
10: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/4 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
10: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/5 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
10: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/6 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
10: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/7 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
10: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
10: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (1 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/9 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
10: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
10: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/11 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
10: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/12 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
10: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/13 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
10: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
10: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (1 ms)
10: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/15 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
10: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/16 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
10: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/17 (1 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
10: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/18 (0 ms total)
10:
10: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
10: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
10: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
10: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
10: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
10: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
10: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
10: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
10: [----------] 9 tests from ArrayRefTest/19 (0 ms total)
10:
10: [----------] 2 tests from CStringUtilityTest
10: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
10: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
10: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
10: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
10: [----------] 2 tests from CStringUtilityTest (0 ms total)
10:
10: [----------] 2 tests from DefaultInitializationAllocator
10: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
10: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
10: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
10: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
10: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
10:
10: [----------] 4 tests from EnumerationHelpersTest
10: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
10: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
10: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
10: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
10: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
10: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
10: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
10: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
10: [----------] 4 tests from EnumerationHelpersTest (0 ms total)
10:
10: [----------] 9 tests from FixedCapacityVectorTest
10: [ RUN ] FixedCapacityVectorTest.IsEmpty
10: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
10: [ RUN ] FixedCapacityVectorTest.PushWorks
10: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.PopWorks
10: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ClearWorks
10: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
10: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.AtThrows
10: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms)
10: [ RUN ] FixedCapacityVectorTest.IteratorWorks
10: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
10: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
10: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
10: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
10: [----------] 9 tests from FixedCapacityVectorTest (0 ms total)
10:
10: [----------] 5 tests from InMemorySerializerTest
10: [ RUN ] InMemorySerializerTest.Roundtrip
10: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
10: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
10: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
10: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
10: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
10: [ RUN ] InMemorySerializerTest.SizeIsCorrect
10: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
10: [----------] 5 tests from InMemorySerializerTest (1 ms total)
10:
10: [----------] 4 tests from KeyValueTreeSerializerTest
10: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
10: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms)
10: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
10: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms)
10: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
10: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms)
10: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
10: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms)
10: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total)
10:
10: [----------] 6 tests from TreeValueTransformTest
10: [ RUN ] TreeValueTransformTest.SimpleTransforms
10: [ OK ] TreeValueTransformTest.SimpleTransforms (1 ms)
10: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
10: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms)
10: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
10: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms)
10: [ RUN ] TreeValueTransformTest.ObjectFromString
10: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms)
10: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
10: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms)
10: [ RUN ] TreeValueTransformTest.ScopedTransformRules
10: [ OK ] TreeValueTransformTest.ScopedTransformRules (1 ms)
10: [----------] 6 tests from TreeValueTransformTest (3 ms total)
10:
10: [----------] 1 test from TreeValueTransformErrorTest
10: [ RUN ] TreeValueTransformErrorTest.ConversionError
10: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms)
10: [----------] 1 test from TreeValueTransformErrorTest (0 ms total)
10:
10: [----------] 9 tests from ListOfLists
10: [ RUN ] ListOfLists.EmptyListOfListsWorks
10: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms)
10: [ RUN ] ListOfLists.AppendWorks
10: [ OK ] ListOfLists.AppendWorks (0 ms)
10: [ RUN ] ListOfLists.EmptyListWorks
10: [ OK ] ListOfLists.EmptyListWorks (0 ms)
10: [ RUN ] ListOfLists.AppendAccessWorks
10: [ OK ] ListOfLists.AppendAccessWorks (0 ms)
10: [ RUN ] ListOfLists.ClearWorks
10: [ OK ] ListOfLists.ClearWorks (0 ms)
10: [ RUN ] ListOfLists.OutOfRangeAccessThrows
10: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms)
10: [ RUN ] ListOfLists.FrontAndBackWork
10: [ OK ] ListOfLists.FrontAndBackWork (1 ms)
10: [ RUN ] ListOfLists.ExtractsAndRestores
10: [ OK ] ListOfLists.ExtractsAndRestores (0 ms)
10: [ RUN ] ListOfLists.AppendsListOfListsWithOffset
10: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms)
10: [----------] 9 tests from ListOfLists (1 ms total)
10:
10: [----------] 7 tests from LoggerTest
10: [ RUN ] LoggerTest.EmptyLoggerWorks
10: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
10: [ RUN ] LoggerTest.LogsToStream
10: [ OK ] LoggerTest.LogsToStream (0 ms)
10: [ RUN ] LoggerTest.LogsToFile
10: [ OK ] LoggerTest.LogsToFile (1 ms)
10: [ RUN ] LoggerTest.LevelFilteringWorks
10: [ OK ] LoggerTest.LevelFilteringWorks (0 ms)
10: [ RUN ] LoggerTest.LogsToMultipleStreams
10: [ OK ] LoggerTest.LogsToMultipleStreams (1 ms)
10: [ RUN ] LoggerTest.LogsToMultipleFiles
10: [ OK ] LoggerTest.LogsToMultipleFiles (2 ms)
10: [ RUN ] LoggerTest.LogsToStreamAndFile
10: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms)
10: [----------] 7 tests from LoggerTest (6 ms total)
10:
10: [----------] 4 tests from MDModuleNotificationTest
10: [ RUN ] MDModuleNotificationTest.addConsumer
10: [ OK ] MDModuleNotificationTest.addConsumer (0 ms)
10: [ RUN ] MDModuleNotificationTest.addConsumerWithPointerParameter
10: [ OK ] MDModuleNotificationTest.addConsumerWithPointerParameter (0 ms)
10: [ RUN ] MDModuleNotificationTest.addTwoDifferentConsumers
10: [ OK ] MDModuleNotificationTest.addTwoDifferentConsumers (0 ms)
10: [ RUN ] MDModuleNotificationTest.consumerOfTwoResources
10: [ OK ] MDModuleNotificationTest.consumerOfTwoResources (0 ms)
10: [----------] 4 tests from MDModuleNotificationTest (0 ms total)
10:
10: [----------] 4 tests from MutexBasicTest
10: [ RUN ] MutexBasicTest.CanBeMade
10: [ OK ] MutexBasicTest.CanBeMade (0 ms)
10: [ RUN ] MutexBasicTest.CanBeLocked
10: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
10: [ RUN ] MutexBasicTest.CanBeTryLocked
10: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
10: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
10: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
10: [----------] 4 tests from MutexBasicTest (0 ms total)
10:
10: [----------] 3 tests from MutexTaskTest
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (9 ms)
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (1 ms)
10: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
10: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
10: [----------] 3 tests from MutexTaskTest (10 ms total)
10:
10: [----------] 2 tests from PathTest
10: [ RUN ] PathTest.StripSourcePrefixWorks
10: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
10: [ RUN ] PathTest.SearchOperationsWork
10: [ OK ] PathTest.SearchOperationsWork (1 ms)
10: [----------] 2 tests from PathTest (1 ms total)
10:
10: [----------] 2 tests from PhysicalNodeCommunicatorTest
10: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
10: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
10: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
10: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
10: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
10:
10: [----------] 5 tests from Range
10: [ RUN ] Range.EmptyRangeWorks
10: [ OK ] Range.EmptyRangeWorks (0 ms)
10: [ RUN ] Range.NonEmptyRangeWorks
10: [ OK ] Range.NonEmptyRangeWorks (0 ms)
10: [ RUN ] Range.BeginEnd
10: [ OK ] Range.BeginEnd (0 ms)
10: [ RUN ] Range.IsInRangeWorks
10: [ OK ] Range.IsInRangeWorks (0 ms)
10: [ RUN ] Range.IteratorWorks
10: [ OK ] Range.IteratorWorks (0 ms)
10: [----------] 5 tests from Range (0 ms total)
10:
10: [----------] 7 tests from StringConvert
10: [ RUN ] StringConvert.NoResultFromEptyString
10: [ OK ] StringConvert.NoResultFromEptyString (0 ms)
10: [ RUN ] StringConvert.ThreeFloatsSuccessfully
10: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms)
10: [ RUN ] StringConvert.OneIntSucessfully
10: [ OK ] StringConvert.OneIntSucessfully (0 ms)
10: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows
10: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms)
10: [ RUN ] StringConvert.ThrowsWhenWrongSize
10: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms)
10: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows
10: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms)
10: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay
10: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms)
10: [----------] 7 tests from StringConvert (0 ms total)
10:
10: [----------] 9 tests from StringUtilityTest
10: [ RUN ] StringUtilityTest.StartsWith
10: [ OK ] StringUtilityTest.StartsWith (0 ms)
10: [ RUN ] StringUtilityTest.EndsWith
10: [ OK ] StringUtilityTest.EndsWith (0 ms)
10: [ RUN ] StringUtilityTest.StripSuffixIfPresent
10: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
10: [ RUN ] StringUtilityTest.StripString
10: [ OK ] StringUtilityTest.StripString (0 ms)
10: [ RUN ] StringUtilityTest.SplitString
10: [ OK ] StringUtilityTest.SplitString (0 ms)
10: [ RUN ] StringUtilityTest.SplitDelimitedString
10: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms)
10: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
10: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
10: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
10: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
10: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
10: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
10: [----------] 9 tests from StringUtilityTest (2 ms total)
10:
10: [----------] 2 tests from FormatStringTest
10: [ RUN ] FormatStringTest.HandlesBasicFormatting
10: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
10: [ RUN ] FormatStringTest.HandlesLongStrings
10: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
10: [----------] 2 tests from FormatStringTest (0 ms total)
10:
10: [----------] 1 test from StringFormatterTest
10: [ RUN ] StringFormatterTest.HandlesBasicFormatting
10: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
10: [----------] 1 test from StringFormatterTest (0 ms total)
10:
10: [----------] 1 test from formatAndJoinTest
10: [ RUN ] formatAndJoinTest.Works
10: [ OK ] formatAndJoinTest.Works (0 ms)
10: [----------] 1 test from formatAndJoinTest (0 ms total)
10:
10: [----------] 1 test from JoinStringsTest
10: [ RUN ] JoinStringsTest.Works
10: [ OK ] JoinStringsTest.Works (0 ms)
10: [----------] 1 test from JoinStringsTest (0 ms total)
10:
10: [----------] 6 tests from ReplaceAllTest
10: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
10: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesNoMatches
10: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
10: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
10: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
10: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
10: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
10: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
10: [----------] 6 tests from ReplaceAllTest (1 ms total)
10:
10: [----------] 10 tests from TextLineWrapperTest
10: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
10: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
10: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
10: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectly
10: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
10: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesIndent
10: [ OK ] TextLineWrapperTest.HandlesIndent (1 ms)
10: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
10: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
10: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
10: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
10: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms)
10: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
10: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
10: [----------] 10 tests from TextLineWrapperTest (1 ms total)
10:
10: [----------] 1 test from TemplateMPTest
10: [ RUN ] TemplateMPTest.DispatchTemplatedFunction
10: [ OK ] TemplateMPTest.DispatchTemplatedFunction (0 ms)
10: [----------] 1 test from TemplateMPTest (0 ms total)
10:
10: [----------] 6 tests from TextWriterTest
10: [ RUN ] TextWriterTest.WritesLines
10: [ OK ] TextWriterTest.WritesLines (0 ms)
10: [ RUN ] TextWriterTest.WritesLinesInParts
10: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
10: [ RUN ] TextWriterTest.WritesWrappedLines
10: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
10: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
10: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
10: [ RUN ] TextWriterTest.TracksNewlines
10: [ OK ] TextWriterTest.TracksNewlines (1 ms)
10: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
10: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
10: [----------] 6 tests from TextWriterTest (1 ms total)
10:
10: [----------] 1 test from TypeTraitsTest
10: [ RUN ] TypeTraitsTest.IsIntegralConstant
10: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
10: [----------] 1 test from TypeTraitsTest (0 ms total)
10:
10: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
10: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
10: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
10: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total)
10:
10: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
10: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
10: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
10: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total)
10:
10: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
10: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
10: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
10: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total)
10:
10: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (1 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (1 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
10: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
10: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
10: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (2 ms total)
10:
10: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
10: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
10: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
10: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 373 tests from 61 test cases ran. (49 ms total)
10: [ PASSED ] 373 tests.
10/65 Test #10: UtilityUnitTests ...................... Passed 0.12 sec
test 11
Start 11: UtilityMpiUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 2 tests from 1 test case.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from PhysicalNodeCommunicatorTest
11: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
11: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (2 ms)
11: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
11: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (16 ms)
11: [----------] 2 tests from PhysicalNodeCommunicatorTest (18 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 2 tests from 1 test case ran. (18 ms total)
11: [ PASSED ] 2 tests.
11/65 Test #11: UtilityMpiUnitTests ................... Passed 0.05 sec
test 12
Start 12: MdlibUnitTest
12: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml"
12: Test timeout computed to be: 30
12: No protocol specified
12: [==========] Running 141 tests from 15 test cases.
12: [----------] Global test environment set-up.
12: [----------] 1 test from VerletBufferConstraintTest
12: [ RUN ] VerletBufferConstraintTest.EqualMasses
12: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
12: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
12:
12: [----------] 2 tests from PrEbinTest
12: [ RUN ] PrEbinTest.HandlesAverages
12: [ OK ] PrEbinTest.HandlesAverages (1 ms)
12: [ RUN ] PrEbinTest.HandlesEmptyAverages
12: [ OK ] PrEbinTest.HandlesEmptyAverages (1 ms)
12: [----------] 2 tests from PrEbinTest (2 ms total)
12:
12: [----------] 3 tests from EnergyDriftTracker
12: [ RUN ] EnergyDriftTracker.emptyWorks
12: [ OK ] EnergyDriftTracker.emptyWorks (0 ms)
12: [ RUN ] EnergyDriftTracker.onePointWorks
12: [ OK ] EnergyDriftTracker.onePointWorks (0 ms)
12: [ RUN ] EnergyDriftTracker.manyPointsWorks
12: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms)
12: [----------] 3 tests from EnergyDriftTracker (1 ms total)
12:
12: [----------] 4 tests from ShakeTest
12: [ RUN ] ShakeTest.ConstrainsOneBond
12: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
12: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
12: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
12: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
12: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
12: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
12: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
12: [----------] 4 tests from ShakeTest (3 ms total)
12:
12: [----------] 1 test from NullSignalTest
12: [ RUN ] NullSignalTest.NullSignallerWorks
12: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
12: [----------] 1 test from NullSignalTest (1 ms total)
12:
12: [----------] 7 tests from SignalTest
12: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
12: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
12: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
12: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
12: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
12: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
12: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
12: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
12: [----------] 7 tests from SignalTest (3 ms total)
12:
12: [----------] 9 tests from UpdateGroups
12: [ RUN ] UpdateGroups.ethaneUA
12: [ OK ] UpdateGroups.ethaneUA (0 ms)
12: [ RUN ] UpdateGroups.methane
12: [ OK ] UpdateGroups.methane (0 ms)
12: [ RUN ] UpdateGroups.ethane
12: [ OK ] UpdateGroups.ethane (0 ms)
12: [ RUN ] UpdateGroups.butaneUA
12: [ OK ] UpdateGroups.butaneUA (0 ms)
12: [ RUN ] UpdateGroups.waterThreeSite
12: [ OK ] UpdateGroups.waterThreeSite (0 ms)
12: [ RUN ] UpdateGroups.waterFourSite
12: [ OK ] UpdateGroups.waterFourSite (0 ms)
12: [ RUN ] UpdateGroups.fourAtomsWithSettle
12: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
12: [ RUN ] UpdateGroups.waterFlexAngle
12: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
12: [ RUN ] UpdateGroups.twoMoltypes
12: [ OK ] UpdateGroups.twoMoltypes (0 ms)
12: [----------] 9 tests from UpdateGroups (5 ms total)
12:
12: [----------] 1 test from UpdateGroupsCog
12: [ RUN ] UpdateGroupsCog.ComputesCogs
12: [ OK ] UpdateGroupsCog.ComputesCogs (3 ms)
12: [----------] 1 test from UpdateGroupsCog (4 ms total)
12:
12: [----------] 12 tests from WithParameters/ConstraintsTest
12: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
12: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
12: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
12: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
12: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (1 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
12: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms)
12: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
12: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms)
12: [----------] 12 tests from WithParameters/ConstraintsTest (10 ms total)
12:
12: [----------] 11 tests from WithParameters/EnergyOutputTest
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (117 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (4 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (6 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
12: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (2 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file
12:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (25 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (6 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (7 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (8 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (8 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (7 ms)
12: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
12: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file
12:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (8 ms)
12: [----------] 11 tests from WithParameters/EnergyOutputTest (212 ms total)
12:
12: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (1 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms)
12: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7
12: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms)
12: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (9 ms total)
12:
12: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (1 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms)
12: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13
12: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms)
12: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (5 ms total)
12:
12: [----------] 23 tests from WithParameters/FreeEnergyParameterTest
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (1 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms)
12: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22
12: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms)
12: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (11 ms total)
12:
12: [----------] 16 tests from WithParameters/LeapFrogTest
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (6 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (19 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (5 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (5 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (5 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (5 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (5 ms)
12: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
12: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (5 ms)
12: [----------] 16 tests from WithParameters/LeapFrogTest (74 ms total)
12:
12: [----------] 13 tests from WithParameters/SettleTest
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (3 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (2 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (1 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (3 ms)
12: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
12: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (3 ms)
12: [----------] 13 tests from WithParameters/SettleTest (27 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 141 tests from 15 test cases ran. (374 ms total)
12: [ PASSED ] 141 tests.
12/65 Test #12: MdlibUnitTest ......................... Passed 0.44 sec
test 13
Start 13: AwhTest
13: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AwhTest.xml"
13: Test timeout computed to be: 30
13: [==========] Running 17 tests from 6 test cases.
13: [----------] Global test environment set-up.
13: [----------] 1 test from BiasTest
13: [ RUN ] BiasTest.DetectsCovering
13: [ OK ] BiasTest.DetectsCovering (2 ms)
13: [----------] 1 test from BiasTest (2 ms total)
13:
13: [----------] 1 test from biasGridTest
13: [ RUN ] biasGridTest.neighborhood
13: [ OK ] biasGridTest.neighborhood (4 ms)
13: [----------] 1 test from biasGridTest (4 ms total)
13:
13: [----------] 1 test from BiasFepLambdaStateTest
13: [ RUN ] BiasFepLambdaStateTest.DetectsCovering
13: [ OK ] BiasFepLambdaStateTest.DetectsCovering (7 ms)
13: [----------] 1 test from BiasFepLambdaStateTest (7 ms total)
13:
13: [----------] 8 tests from WithParameters/BiasTest
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (0 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms)
13: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
13: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms)
13: [----------] 8 tests from WithParameters/BiasTest (9 ms total)
13:
13: [----------] 2 tests from WithParameters/BiasStateTest
13: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
13: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms)
13: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
13: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms)
13: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total)
13:
13: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (16 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (16 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (16 ms)
13: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3
13: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (16 ms)
13: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (68 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 17 tests from 6 test cases ran. (91 ms total)
13: [ PASSED ] 17 tests.
13/65 Test #13: AwhTest ............................... Passed 0.12 sec
test 14
Start 14: DensityFittingAppliedForcesUnitTest
14: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml"
14: Test timeout computed to be: 30
14: [==========] Running 18 tests from 4 test cases.
14: [----------] Global test environment set-up.
14: [----------] 2 tests from DensityFittingTest
14: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
14: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (2 ms)
14: [ RUN ] DensityFittingTest.SingleAtom
14: [ OK ] DensityFittingTest.SingleAtom (1 ms)
14: [----------] 2 tests from DensityFittingTest (3 ms total)
14:
14: [----------] 7 tests from DensityFittingAmplitudeLookupTest
14: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
14: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
14: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
14: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
14: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
14: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
14: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
14: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
14: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
14: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total)
14:
14: [----------] 1 test from DensityFittingForceProviderState
14: [ RUN ] DensityFittingForceProviderState.RoundTripSaving
14: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms)
14: [----------] 1 test from DensityFittingForceProviderState (0 ms total)
14:
14: [----------] 8 tests from DensityFittingOptionsTest
14: [ RUN ] DensityFittingOptionsTest.DefaultParameters
14: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
14: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
14: [ OK ] DensityFittingOptionsTest.OptionSetsActive (1 ms)
14: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
14: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms)
14: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
14: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms)
14: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
14: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (1 ms)
14: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
14: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
14: [ RUN ] DensityFittingOptionsTest.KvtToInternal
14: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms)
14: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
14: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (1 ms)
14: [----------] 8 tests from DensityFittingOptionsTest (4 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 18 tests from 4 test cases ran. (7 ms total)
14: [ PASSED ] 18 tests.
14/65 Test #14: DensityFittingAppliedForcesUnitTest ... Passed 0.05 sec
test 15
Start 15: AppliedForcesUnitTest
15: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml"
15: Test timeout computed to be: 30
15: [==========] Running 3 tests from 1 test case.
15: [----------] Global test environment set-up.
15: [----------] 3 tests from ElectricFieldTest
15: [ RUN ] ElectricFieldTest.Static
15: [ OK ] ElectricFieldTest.Static (1 ms)
15: [ RUN ] ElectricFieldTest.Oscillating
15: [ OK ] ElectricFieldTest.Oscillating (0 ms)
15: [ RUN ] ElectricFieldTest.Pulsed
15: [ OK ] ElectricFieldTest.Pulsed (0 ms)
15: [----------] 3 tests from ElectricFieldTest (1 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 3 tests from 1 test case ran. (1 ms total)
15: [ PASSED ] 3 tests.
15/65 Test #15: AppliedForcesUnitTest ................. Passed 0.04 sec
test 16
Start 16: ListedForcesTest
16: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ListedForcesTest.xml"
16: Test timeout computed to be: 30
16: [==========] Running 111 tests from 7 test cases.
16: [----------] Global test environment set-up.
16: [----------] 24 tests from Bond/ListedForcesTest
16: [ RUN ] Bond/ListedForcesTest.Ifunc/0
16: [ OK ] Bond/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/1
16: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/2
16: [ OK ] Bond/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/3
16: [ OK ] Bond/ListedForcesTest.Ifunc/3 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/4
16: [ OK ] Bond/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/5
16: [ OK ] Bond/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/6
16: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/7
16: [ OK ] Bond/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/8
16: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/9
16: [ OK ] Bond/ListedForcesTest.Ifunc/9 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/10
16: [ OK ] Bond/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/11
16: [ OK ] Bond/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/12
16: [ OK ] Bond/ListedForcesTest.Ifunc/12 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/13
16: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/14
16: [ OK ] Bond/ListedForcesTest.Ifunc/14 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/15
16: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/16
16: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/17
16: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/18
16: [ OK ] Bond/ListedForcesTest.Ifunc/18 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/19
16: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/20
16: [ OK ] Bond/ListedForcesTest.Ifunc/20 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/21
16: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/22
16: [ OK ] Bond/ListedForcesTest.Ifunc/22 (1 ms)
16: [ RUN ] Bond/ListedForcesTest.Ifunc/23
16: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms)
16: [----------] 24 tests from Bond/ListedForcesTest (16 ms total)
16:
16: [----------] 33 tests from Angle/ListedForcesTest
16: [ RUN ] Angle/ListedForcesTest.Ifunc/0
16: [ OK ] Angle/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/1
16: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/2
16: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/3
16: [ OK ] Angle/ListedForcesTest.Ifunc/3 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/4
16: [ OK ] Angle/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/5
16: [ OK ] Angle/ListedForcesTest.Ifunc/5 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/6
16: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/7
16: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/8
16: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/9
16: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/10
16: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/11
16: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/12
16: [ OK ] Angle/ListedForcesTest.Ifunc/12 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/13
16: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/14
16: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/15
16: [ OK ] Angle/ListedForcesTest.Ifunc/15 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/16
16: [ OK ] Angle/ListedForcesTest.Ifunc/16 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/17
16: [ OK ] Angle/ListedForcesTest.Ifunc/17 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/18
16: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/19
16: [ OK ] Angle/ListedForcesTest.Ifunc/19 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/20
16: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/21
16: [ OK ] Angle/ListedForcesTest.Ifunc/21 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/22
16: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/23
16: [ OK ] Angle/ListedForcesTest.Ifunc/23 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/24
16: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/25
16: [ OK ] Angle/ListedForcesTest.Ifunc/25 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/26
16: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/27
16: [ OK ] Angle/ListedForcesTest.Ifunc/27 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/28
16: [ OK ] Angle/ListedForcesTest.Ifunc/28 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/29
16: [ OK ] Angle/ListedForcesTest.Ifunc/29 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/30
16: [ OK ] Angle/ListedForcesTest.Ifunc/30 (1 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/31
16: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms)
16: [ RUN ] Angle/ListedForcesTest.Ifunc/32
16: [ OK ] Angle/ListedForcesTest.Ifunc/32 (1 ms)
16: [----------] 33 tests from Angle/ListedForcesTest (23 ms total)
16:
16: [----------] 18 tests from Dihedral/ListedForcesTest
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (1 ms)
16: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17
16: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms)
16: [----------] 18 tests from Dihedral/ListedForcesTest (13 ms total)
16:
16: [----------] 12 tests from Polarize/ListedForcesTest
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/0
16: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/1
16: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/2
16: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/3
16: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/4
16: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/5
16: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/6
16: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/7
16: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/8
16: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/9
16: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/10
16: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (1 ms)
16: [ RUN ] Polarize/ListedForcesTest.Ifunc/11
16: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms)
16: [----------] 12 tests from Polarize/ListedForcesTest (6 ms total)
16:
16: [----------] 18 tests from Restraints/ListedForcesTest
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/0
16: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/1
16: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/2
16: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/3
16: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/4
16: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/5
16: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/6
16: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/7
16: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/8
16: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/9
16: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/10
16: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/11
16: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/12
16: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/13
16: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/14
16: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/15
16: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/16
16: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (1 ms)
16: [ RUN ] Restraints/ListedForcesTest.Ifunc/17
16: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (1 ms)
16: [----------] 18 tests from Restraints/ListedForcesTest (13 ms total)
16:
16: [----------] 3 tests from BondZeroLength/ListedForcesTest
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (1 ms)
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms)
16: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2
16: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (1 ms)
16: [----------] 3 tests from BondZeroLength/ListedForcesTest (2 ms total)
16:
16: [----------] 3 tests from AngleZero/ListedForcesTest
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms)
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (1 ms)
16: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2
16: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms)
16: [----------] 3 tests from AngleZero/ListedForcesTest (1 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 111 tests from 7 test cases ran. (74 ms total)
16: [ PASSED ] 111 tests.
16/65 Test #16: ListedForcesTest ...................... Passed 0.14 sec
test 17
Start 17: CommandLineUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 59 tests from 7 test cases.
17: [----------] Global test environment set-up.
17: [----------] 3 tests from CommandLineHelpModuleTest
17: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
17: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (2 ms)
17: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
17: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
17: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
17: [ OK ] CommandLineHelpModuleTest.ExportsHelp (3 ms)
17: [----------] 3 tests from CommandLineHelpModuleTest (7 ms total)
17:
17: [----------] 7 tests from CommandLineHelpWriterTest
17: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
17: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
17: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
17: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
17: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
17: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
17: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms)
17: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
17: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (1 ms)
17: [----------] 7 tests from CommandLineHelpWriterTest (5 ms total)
17:
17: [----------] 6 tests from CommandLineModuleManagerTest
17: [ RUN ] CommandLineModuleManagerTest.RunsModule
17: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
17: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms)
17: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
17: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms)
17: [----------] 6 tests from CommandLineModuleManagerTest (2 ms total)
17:
17: [----------] 13 tests from CommandLineParserTest
17: [ RUN ] CommandLineParserTest.HandlesSingleValues
17: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
17: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
17: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (1 ms)
17: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
17: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
17: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesString
17: [ OK ] CommandLineParserTest.HandlesString (0 ms)
17: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
17: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
17: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
17: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
17: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
17: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
17: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
17: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
17: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
17: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
17: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
17: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
17: [----------] 13 tests from CommandLineParserTest (2 ms total)
17:
17: [----------] 6 tests from CommandLineProgramContextTest
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (1 ms)
17: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
17: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
17: [----------] 6 tests from CommandLineProgramContextTest (1 ms total)
17:
17: [----------] 3 tests from OutputNamesTest
17: [ RUN ] OutputNamesTest.CanBeSuffixed
17: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
17: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
17: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
17: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
17: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
17: [----------] 3 tests from OutputNamesTest (0 ms total)
17:
17: [----------] 21 tests from ParseCommonArgsTest
17: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
17: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
17: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
17: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
17: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
17: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
17: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
17: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
17: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
17: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
17: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
17: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (1 ms)
17: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
17: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
17: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
17: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
17: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
17: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms)
17: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
17: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms)
17: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
17: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (1 ms)
17: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
17: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms)
17: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
17: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (3 ms)
17: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
17: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (2 ms)
17: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
17: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
17: [----------] 21 tests from ParseCommonArgsTest (11 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 59 tests from 7 test cases ran. (28 ms total)
17: [ PASSED ] 59 tests.
17/65 Test #17: CommandLineUnitTests .................. Passed 0.07 sec
test 18
Start 18: DomDecTests
18: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DomDecTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 9 tests from 2 test cases.
18: [----------] Global test environment set-up.
18: [----------] 7 tests from HashedMap
18: [ RUN ] HashedMap.InsertsFinds
18: [ OK ] HashedMap.InsertsFinds (0 ms)
18: [ RUN ] HashedMap.NegativeKeysWork
18: [ OK ] HashedMap.NegativeKeysWork (0 ms)
18: [ RUN ] HashedMap.InsertsErases
18: [ OK ] HashedMap.InsertsErases (0 ms)
18: [ RUN ] HashedMap.InsertsOrAssigns
18: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
18: [ RUN ] HashedMap.Clears
18: [ OK ] HashedMap.Clears (0 ms)
18: [ RUN ] HashedMap.LinkedEntries
18: [ OK ] HashedMap.LinkedEntries (0 ms)
18: [ RUN ] HashedMap.ResizesTable
18: [ OK ] HashedMap.ResizesTable (0 ms)
18: [----------] 7 tests from HashedMap (0 ms total)
18:
18: [----------] 2 tests from LocalAtomSetManager
18: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
18: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
18: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
18: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
18: [----------] 2 tests from LocalAtomSetManager (0 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 9 tests from 2 test cases ran. (1 ms total)
18: [ PASSED ] 9 tests.
18/65 Test #18: DomDecTests ........................... Passed 0.05 sec
test 19
Start 19: DomDecMpiTests
19: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml"
19: Test timeout computed to be: 30
19: No protocol specified
19: [==========] Running 4 tests from 1 test case.
19: [----------] Global test environment set-up.
19: [----------] 4 tests from HaloExchangeTest
19: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse
19: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (1 ms)
19: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses
19: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (32 ms)
19: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim
19: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (10 ms)
19: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1
19: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (10 ms)
19: [----------] 4 tests from HaloExchangeTest (53 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 4 tests from 1 test case ran. (53 ms total)
19: [ PASSED ] 4 tests.
19/65 Test #19: DomDecMpiTests ........................ Passed 0.12 sec
test 20
Start 20: EwaldUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml"
20: Test timeout computed to be: 30
20: No protocol specified
20: [==========] Running 185 tests from 10 test cases.
20: [----------] Global test environment set-up.
20: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (12 ms)
20: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
20: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
20: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (13 ms total)
20:
20: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (15 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (11 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (12 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (11 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (12 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (15 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (15 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (15 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (14 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (13 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (14 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (14 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (19 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (13 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (12 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (16 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (16 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (16 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (16 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (16 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (17 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (17 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (17 ms)
20: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
20: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (17 ms)
20: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (363 ms total)
20:
20: [----------] 72 tests from SaneInput/PmeGatherTest
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (0 ms)
20: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
20: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms)
20: [----------] 72 tests from SaneInput/PmeGatherTest (65 ms total)
20:
20: [----------] 16 tests from SaneInput/PmeSolveTest
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (5 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (3 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (4 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (2 ms)
20: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
20: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (2 ms)
20: [----------] 16 tests from SaneInput/PmeSolveTest (46 ms total)
20:
20: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (2 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (3 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms)
20: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (2 ms)
20: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (15 ms total)
20:
20: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (4 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (4 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (2 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (2 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (4 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (4 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (2 ms)
20: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (2 ms)
20: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (27 ms total)
20:
20: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (5 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (5 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (5 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (5 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (3 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (2 ms)
20: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
20: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (3 ms)
20: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (53 ms total)
20:
20: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (6 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (5 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (5 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (3 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (4 ms)
20: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (5 ms)
20: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (52 ms total)
20:
20: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (5 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (6 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (7 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (6 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (8 ms)
20: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (8 ms)
20: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (65 ms total)
20:
20: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (9 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (10 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (13 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (12 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (15 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (17 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (8 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (8 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (11 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (11 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (17 ms)
20: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
20: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (23 ms)
20: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (165 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 185 tests from 10 test cases ran. (865 ms total)
20: [ PASSED ] 185 tests.
20/65 Test #20: EwaldUnitTests ........................ Passed 0.99 sec
test 21
Start 21: FFTUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FFTUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 14 tests from 4 test cases.
21: [----------] Global test environment set-up.
21: [----------] 2 tests from ManyFFTTest
21: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
21: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (14 ms)
21: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
21: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (22 ms)
21: [----------] 2 tests from ManyFFTTest (38 ms total)
21:
21: [----------] 1 test from FFTTest
21: [ RUN ] FFTTest.Real2DLength18_15Test
21: [ OK ] FFTTest.Real2DLength18_15Test (7 ms)
21: [----------] 1 test from FFTTest (8 ms total)
21:
21: [----------] 1 test from FFFTest3D
21: [ RUN ] FFFTest3D.Real5_6_9
21: [ OK ] FFFTest3D.Real5_6_9 (6 ms)
21: [----------] 1 test from FFFTest3D (7 ms total)
21:
21: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (2 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (3 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
21: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (4 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (12 ms)
21: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
21: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (20 ms)
21: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (49 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 14 tests from 4 test cases ran. (103 ms total)
21: [ PASSED ] 14 tests.
21/65 Test #21: FFTUnitTests .......................... Passed 0.14 sec
test 22
Start 22: GpuUtilsUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml"
22: Test timeout computed to be: 30
22: No protocol specified
22: [==========] Running 64 tests from 22 test cases.
22: [----------] Global test environment set-up.
22: [----------] 2 tests from ClfftInitializer
22: [ RUN ] ClfftInitializer.SingleInitializationWorks
22: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
22: [ RUN ] ClfftInitializer.TwoInitializationsWork
22: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
22: [----------] 2 tests from ClfftInitializer (1 ms total)
22:
22: [----------] 1 test from DevicesAvailable
22: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice
22: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms)
22: [----------] 1 test from DevicesAvailable (0 ms total)
22:
22: [----------] 1 test from DeviceStreamManagerTest
22: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice
22: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms)
22: [----------] 1 test from DeviceStreamManagerTest (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
22: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double
22: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<double>
22: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
22: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
22: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
22: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
22: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double
22: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/1 (1 ms total)
22:
22: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<double>
22: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
22: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
22: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
22: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
22: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
22: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
22: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.Swap
22: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/0.Comparison
22: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double
22: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
22: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.Swap
22: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/1.Comparison
22: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<double>
22: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
22: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.Swap
22: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/2.Comparison
22: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total)
22:
22: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
22: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
22: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
22: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
22: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.Swap
22: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
22: [ RUN ] HostAllocatorTestNoMem/3.Comparison
22: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
22: [----------] 5 tests from HostAllocatorTestNoMem/3 (1 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
22: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double
22: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
22:
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<double>
22: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
22: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
22: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
22: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
22: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
22:
22: [----------] 1 test from HostAllocatorUntypedTest
22: [ RUN ] HostAllocatorUntypedTest.Comparison
22: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
22: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
22: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/0.Move
22: [ OK ] AllocatorTest/0.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/0 (1 ms total)
22:
22: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/1.Move
22: [ OK ] AllocatorTest/1.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/1 (0 ms total)
22:
22: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (2 ms)
22: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/2.Move
22: [ OK ] AllocatorTest/2.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/2 (2 ms total)
22:
22: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
22: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
22: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
22: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms)
22: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
22: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
22: [ RUN ] AllocatorTest/3.Move
22: [ OK ] AllocatorTest/3.Move (0 ms)
22: [----------] 4 tests from AllocatorTest/3 (1 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 64 tests from 22 test cases ran. (7 ms total)
22: [ PASSED ] 64 tests.
22/65 Test #22: GpuUtilsUnitTests ..................... Passed 0.09 sec
test 23
Start 23: HardwareUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 6 tests from 3 test cases.
23: [----------] Global test environment set-up.
23: [----------] 1 test from CpuInfoTest
23: [ RUN ] CpuInfoTest.SupportLevel
23: [ OK ] CpuInfoTest.SupportLevel (0 ms)
23: [----------] 1 test from CpuInfoTest (0 ms total)
23:
23: [----------] 4 tests from HardwareTopologyTest
23: [ RUN ] HardwareTopologyTest.Execute
23: No protocol specified
23: [ OK ] HardwareTopologyTest.Execute (34 ms)
23: [ RUN ] HardwareTopologyTest.HwlocExecute
23: No protocol specified
23: [ OK ] HardwareTopologyTest.HwlocExecute (29 ms)
23: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
23: No protocol specified
23: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (20 ms)
23: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
23: No protocol specified
23: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (20 ms)
23: [----------] 4 tests from HardwareTopologyTest (103 ms total)
23:
23: [----------] 1 test from DevicesManagerTest
23: [ RUN ] DevicesManagerTest.Serialization
23: [ OK ] DevicesManagerTest.Serialization (0 ms)
23: [----------] 1 test from DevicesManagerTest (0 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 6 tests from 3 test cases ran. (104 ms total)
23: [ PASSED ] 6 tests.
23/65 Test #23: HardwareUnitTests ..................... Passed 0.15 sec
test 24
Start 24: MathUnitTests
24: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MathUnitTests.xml"
24: Test timeout computed to be: 30
24: [==========] Running 292 tests from 32 test cases.
24: [----------] Global test environment set-up.
24: [----------] 1 test from EmptyArrayRefWithPaddingTest
24: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
24: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
24: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
24:
24: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
24: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
24: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
24: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
24: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
24: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
24:
24: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
24: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
24: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
24: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
24: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
24: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
24:
24: [----------] 11 tests from TranslateAndScaleTest
24: [ RUN ] TranslateAndScaleTest.identityTransformation
24: [ OK ] TranslateAndScaleTest.identityTransformation (1 ms)
24: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
24: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
24: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
24: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
24: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
24: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector
24: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingIdentity
24: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
24: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector
24: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
24: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (1 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
24: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
24: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector
24: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms)
24: [----------] 11 tests from TranslateAndScaleTest (2 ms total)
24:
24: [----------] 2 tests from AffineTransformationTest
24: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors
24: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms)
24: [ RUN ] AffineTransformationTest.applyTransformationToVectors
24: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms)
24: [----------] 2 tests from AffineTransformationTest (0 ms total)
24:
24: [----------] 12 tests from DensitySimilarityTest
24: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
24: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
24: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
24: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms)
24: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
24: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
24: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
24: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
24: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
24: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
24: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
24: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (1 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
24: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (118 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
24: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (145 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
24: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (56 ms)
24: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
24: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (1 ms)
24: [----------] 12 tests from DensitySimilarityTest (321 ms total)
24:
24: [----------] 6 tests from StructureSimilarityTest
24: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
24: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
24: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
24: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
24: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
24: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
24: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
24: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
24: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
24: [----------] 6 tests from StructureSimilarityTest (0 ms total)
24:
24: [----------] 8 tests from ExponentialMovingAverage
24: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
24: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
24: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
24: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
24: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
24: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
24: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
24: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
24: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
24: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
24: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
24: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
24: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
24: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
24: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
24: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
24: [----------] 8 tests from ExponentialMovingAverage (0 ms total)
24:
24: [----------] 21 tests from FunctionTest
24: [ RUN ] FunctionTest.StaticLog2
24: [ OK ] FunctionTest.StaticLog2 (0 ms)
24: [ RUN ] FunctionTest.Log2I32Bit
24: [ OK ] FunctionTest.Log2I32Bit (0 ms)
24: [ RUN ] FunctionTest.Log2I64Bit
24: [ OK ] FunctionTest.Log2I64Bit (0 ms)
24: [ RUN ] FunctionTest.GreatestCommonDivisor
24: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
24: [ RUN ] FunctionTest.InvsqrtFloat
24: [ OK ] FunctionTest.InvsqrtFloat (1 ms)
24: [ RUN ] FunctionTest.InvsqrtDouble
24: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
24: [ RUN ] FunctionTest.InvsqrtInteger
24: [ OK ] FunctionTest.InvsqrtInteger (0 ms)
24: [ RUN ] FunctionTest.InvcbrtFloat
24: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
24: [ RUN ] FunctionTest.InvcbrtDouble
24: [ OK ] FunctionTest.InvcbrtDouble (0 ms)
24: [ RUN ] FunctionTest.InvcbrtInteger
24: [ OK ] FunctionTest.InvcbrtInteger (1 ms)
24: [ RUN ] FunctionTest.SixthrootFloat
24: [ OK ] FunctionTest.SixthrootFloat (0 ms)
24: [ RUN ] FunctionTest.SixthrootDouble
24: [ OK ] FunctionTest.SixthrootDouble (0 ms)
24: [ RUN ] FunctionTest.SixthrootInteger
24: [ OK ] FunctionTest.SixthrootInteger (0 ms)
24: [ RUN ] FunctionTest.InvsixthrootFloat
24: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
24: [ RUN ] FunctionTest.InvsixthrootDouble
24: [ OK ] FunctionTest.InvsixthrootDouble (1 ms)
24: [ RUN ] FunctionTest.InvsixthrootInteger
24: [ OK ] FunctionTest.InvsixthrootInteger (0 ms)
24: [ RUN ] FunctionTest.Powers
24: [ OK ] FunctionTest.Powers (0 ms)
24: [ RUN ] FunctionTest.ErfInvFloat
24: [ OK ] FunctionTest.ErfInvFloat (0 ms)
24: [ RUN ] FunctionTest.ErfInvDouble
24: [ OK ] FunctionTest.ErfInvDouble (0 ms)
24: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
24: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms)
24: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
24: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms)
24: [----------] 21 tests from FunctionTest (5 ms total)
24:
24: [----------] 4 tests from GaussianOn1DLattice
24: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
24: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
24: [ RUN ] GaussianOn1DLattice.isCorrect
24: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
24: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
24: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms)
24: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
24: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
24: [----------] 4 tests from GaussianOn1DLattice (1 ms total)
24:
24: [----------] 9 tests from GaussTransformTest
24: [ RUN ] GaussTransformTest.isZeroUponConstruction
24: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
24: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
24: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
24: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
24: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
24: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
24: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
24: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
24: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
24: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
24: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms)
24: [ RUN ] GaussTransformTest.view
24: [ OK ] GaussTransformTest.view (0 ms)
24: [----------] 9 tests from GaussTransformTest (0 ms total)
24:
24: [----------] 3 tests from DensityFittingForce
24: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
24: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
24: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
24: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
24: [ RUN ] DensityFittingForce.pullsTowardsDerivative
24: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
24: [----------] 3 tests from DensityFittingForce (0 ms total)
24:
24: [----------] 2 tests from InvertMatrixTest
24: [ RUN ] InvertMatrixTest.IdentityIsImpotent
24: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
24: [ RUN ] InvertMatrixTest.ComputesInverse
24: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
24: [----------] 2 tests from InvertMatrixTest (0 ms total)
24:
24: [----------] 2 tests from InvertBoxMatrixTest
24: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
24: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
24: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
24: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
24: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
24:
24: [----------] 17 tests from MatrixTest
24: [ RUN ] MatrixTest.canSetFromArray
24: [ OK ] MatrixTest.canSetFromArray (0 ms)
24: [ RUN ] MatrixTest.canSetStaticallyFromList
24: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
24: [ RUN ] MatrixTest.canConstructAndFill
24: [ OK ] MatrixTest.canConstructAndFill (0 ms)
24: [ RUN ] MatrixTest.canSetValues
24: [ OK ] MatrixTest.canSetValues (0 ms)
24: [ RUN ] MatrixTest.canCopyAssign
24: [ OK ] MatrixTest.canCopyAssign (0 ms)
24: [ RUN ] MatrixTest.canSwap
24: [ OK ] MatrixTest.canSwap (0 ms)
24: [ RUN ] MatrixTest.staticMultiDimArrayExtent
24: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
24: [ RUN ] MatrixTest.determinantWorks
24: [ OK ] MatrixTest.determinantWorks (0 ms)
24: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
24: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
24: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
24: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
24: [ RUN ] MatrixTest.traceWorks
24: [ OK ] MatrixTest.traceWorks (0 ms)
24: [ RUN ] MatrixTest.transposeWorks
24: [ OK ] MatrixTest.transposeWorks (0 ms)
24: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
24: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
24: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
24: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
24: [ RUN ] MatrixTest.canFillLegacyMatrix
24: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
24: [ RUN ] MatrixTest.IdentityMatrix
24: [ OK ] MatrixTest.IdentityMatrix (0 ms)
24: [ RUN ] MatrixTest.MatrixVectorMultiplication
24: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms)
24: [----------] 17 tests from MatrixTest (0 ms total)
24:
24: [----------] 25 tests from MultiDimArrayTest
24: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
24: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
24: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
24: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
24: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
24: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
24: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
24: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
24: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
24: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
24: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
24: [ OK ] MultiDimArrayTest.canCopyAssignStatic (1 ms)
24: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
24: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSwapStatic
24: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
24: [ RUN ] MultiDimArrayTest.canSwapDynamic
24: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
24: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
24: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
24: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
24: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
24: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
24: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
24: [ RUN ] MultiDimArrayTest.conversionToView
24: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
24: [ RUN ] MultiDimArrayTest.conversionToConstView
24: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
24: [ RUN ] MultiDimArrayTest.viewBegin
24: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
24: [ RUN ] MultiDimArrayTest.viewEnd
24: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
24: [ RUN ] MultiDimArrayTest.constViewConstBegin
24: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
24: [ RUN ] MultiDimArrayTest.constViewConstEnd
24: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
24: [----------] 25 tests from MultiDimArrayTest (1 ms total)
24:
24: [----------] 4 tests from MultiDimArrayToMdSpanTest
24: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
24: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
24: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
24: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
24:
24: [----------] 9 tests from NelderMeadSimplexTest
24: [ RUN ] NelderMeadSimplexTest.BestVertex
24: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms)
24: [ RUN ] NelderMeadSimplexTest.WorstVertex
24: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms)
24: [ RUN ] NelderMeadSimplexTest.SecondWorstValue
24: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms)
24: [ RUN ] NelderMeadSimplexTest.ReflectionPoint
24: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint
24: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint
24: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms)
24: [ RUN ] NelderMeadSimplexTest.SwapOutWorst
24: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms)
24: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest
24: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms)
24: [ RUN ] NelderMeadSimplexTest.OrientedLength
24: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms)
24: [----------] 9 tests from NelderMeadSimplexTest (0 ms total)
24:
24: [----------] 2 tests from NelderMead
24: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly
24: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (1 ms)
24: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly
24: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms)
24: [----------] 2 tests from NelderMead (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
24: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ResizeWorks
24: [ OK ] PaddedVectorTest/0.ResizeWorks (1 ms)
24: [ RUN ] PaddedVectorTest/0.ReserveWorks
24: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanCopyAssign
24: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanMoveAssign
24: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/0.CanSwap
24: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/0 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
24: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ResizeWorks
24: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ReserveWorks
24: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanCopyAssign
24: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanMoveAssign
24: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/1.CanSwap
24: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/1 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
24: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ResizeWorks
24: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ReserveWorks
24: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanCopyAssign
24: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanMoveAssign
24: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/2.CanSwap
24: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/2 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
24: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ResizeWorks
24: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ReserveWorks
24: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanCopyAssign
24: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanMoveAssign
24: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/3.CanSwap
24: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/3 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
24: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ResizeWorks
24: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ReserveWorks
24: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanCopyAssign
24: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanMoveAssign
24: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/4.CanSwap
24: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/4 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ResizeWorks
24: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ReserveWorks
24: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanCopyAssign
24: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanMoveAssign
24: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/5.CanSwap
24: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/5 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ResizeWorks
24: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ReserveWorks
24: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanCopyAssign
24: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanMoveAssign
24: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/6.CanSwap
24: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/6 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ResizeWorks
24: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ReserveWorks
24: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanCopyAssign
24: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanMoveAssign
24: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/7.CanSwap
24: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/7 (1 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ResizeWorks
24: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ReserveWorks
24: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanCopyAssign
24: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanMoveAssign
24: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/8.CanSwap
24: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/8 (0 ms total)
24:
24: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
24: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks
24: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ResizeWorks
24: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ReserveWorks
24: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve
24: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks
24: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks
24: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks
24: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms)
24: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical
24: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanCopyAssign
24: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanMoveAssign
24: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
24: [ RUN ] PaddedVectorTest/9.CanSwap
24: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
24: [----------] 11 tests from PaddedVectorTest/9 (0 ms total)
24:
24: [----------] 37 tests from RVecTest
24: [ RUN ] RVecTest.CanBeStoredInVector
24: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
24: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
24: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
24: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
24: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
24: [ RUN ] RVecTest.WorksAsMutable_rvec
24: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
24: [ RUN ] RVecTest.WorksAs_rvec_Array
24: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
24: [ RUN ] RVecTest.CanAddRVecToRvec
24: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
24: [ RUN ] RVecTest.CanAddAssignRVecToRvec
24: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
24: [ RUN ] RVecTest.CanSubtractRVecFromRvec
24: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
24: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
24: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
24: [ RUN ] RVecTest.CanDotProductRVecByRvec
24: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
24: [ RUN ] RVecTest.CanCrossProductRVecByRvec
24: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
24: [ RUN ] RVecTest.CanDivideRVecInplace
24: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
24: [ RUN ] RVecTest.CanScaleRVec
24: [ OK ] RVecTest.CanScaleRVec (0 ms)
24: [ RUN ] RVecTest.CanDivideRVec
24: [ OK ] RVecTest.CanDivideRVec (0 ms)
24: [ RUN ] RVecTest.CanDoUnitvFromRVec
24: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
24: [ RUN ] RVecTest.CanSqLengthOfRVec
24: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanLengthOfRVec
24: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanCastToRVec
24: [ OK ] RVecTest.CanCastToRVec (0 ms)
24: [ RUN ] RVecTest.CanCastToDVec
24: [ OK ] RVecTest.CanCastToDVec (0 ms)
24: [ RUN ] RVecTest.CanLeftScalarMultiply
24: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
24: [ RUN ] RVecTest.CanRightScalarMultiply
24: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
24: [ RUN ] RVecTest.CanGetUnitvFromRVec
24: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
24: [ RUN ] RVecTest.CanGetSqLengthOfRVec
24: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanGetLengthOfRVec
24: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
24: [ RUN ] RVecTest.CanDoCrossProductOfRVec
24: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
24: [ RUN ] RVecTest.CanDoDotProductOfRVec
24: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
24: [ RUN ] RVecTest.CanScaleByVector
24: [ OK ] RVecTest.CanScaleByVector (0 ms)
24: [ RUN ] RVecTest.asIVec
24: [ OK ] RVecTest.asIVec (0 ms)
24: [ RUN ] RVecTest.elementWiseMin
24: [ OK ] RVecTest.elementWiseMin (0 ms)
24: [ RUN ] RVecTest.elementWiseMax
24: [ OK ] RVecTest.elementWiseMax (0 ms)
24: [ RUN ] RVecTest.WorksAs_dvec_Reference
24: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
24: [ RUN ] RVecTest.WorksAs_ivec_Reference
24: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
24: [ RUN ] RVecTest.WorksAs_rvec_Reference
24: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
24: [ RUN ] RVecTest.CopyConstructorWorks
24: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
24: [ RUN ] RVecTest.CopyAssignmentWorks
24: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
24: [ RUN ] RVecTest.MoveConstructorWorks
24: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
24: [ RUN ] RVecTest.MoveAssignmentWorks
24: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
24: [----------] 37 tests from RVecTest (1 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 292 tests from 32 test cases ran. (337 ms total)
24: [ PASSED ] 292 tests.
24/65 Test #24: MathUnitTests ......................... Passed 0.39 sec
test 25
Start 25: MdrunUtilityUnitTests
25: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml"
25: Test timeout computed to be: 30
25: [==========] Running 17 tests from 1 test case.
25: [----------] Global test environment set-up.
25: [----------] 17 tests from ThreadAffinityTest
25: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
25: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
25: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
25: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (1 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms)
25: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
25: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
25: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms)
25: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
25: NOTE: Affinity setting failed.
25: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
25: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
25: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
25: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms)
25: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
25: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (1 ms)
25: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
25: NOTE: Affinity setting for 1/2 threads failed.
25: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms)
25: [----------] 17 tests from ThreadAffinityTest (10 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 17 tests from 1 test case ran. (10 ms total)
25: [ PASSED ] 17 tests.
25/65 Test #25: MdrunUtilityUnitTests ................. Passed 0.04 sec
test 26
Start 26: MdrunUtilityMpiUnitTests
26: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
26: Test timeout computed to be: 30
26: [==========] Running 13 tests from 2 test cases.
26: [----------] Global test environment set-up.
26: [----------] 6 tests from ThreadAffinityMultiRankTest
26: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
26: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (8 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
26: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (9 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
26: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (3 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
26: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (6 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
26: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (10 ms)
26: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
26: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (2 ms)
26: [----------] 6 tests from ThreadAffinityMultiRankTest (38 ms total)
26:
26: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (9 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (2 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (8 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (3 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (7 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (20 ms)
26: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
26: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (10 ms)
26: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (59 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 13 tests from 2 test cases ran. (98 ms total)
26: [ PASSED ] 13 tests.
26/65 Test #26: MdrunUtilityMpiUnitTests .............. Passed 0.13 sec
test 27
Start 27: MDSpanTests
27: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MDSpanTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 32 tests from 7 test cases.
27: [----------] Global test environment set-up.
27: [----------] 4 tests from BasicAccessorPolicy
27: [ RUN ] BasicAccessorPolicy.Decay
27: [ OK ] BasicAccessorPolicy.Decay (0 ms)
27: [ RUN ] BasicAccessorPolicy.Access
27: [ OK ] BasicAccessorPolicy.Access (0 ms)
27: [ RUN ] BasicAccessorPolicy.Offset
27: [ OK ] BasicAccessorPolicy.Offset (0 ms)
27: [ RUN ] BasicAccessorPolicy.CopyAccessor
27: [ OK ] BasicAccessorPolicy.CopyAccessor (1 ms)
27: [----------] 4 tests from BasicAccessorPolicy (1 ms total)
27:
27: [----------] 4 tests from ExtentsTest
27: [ RUN ] ExtentsTest.Construction
27: [ OK ] ExtentsTest.Construction (0 ms)
27: [ RUN ] ExtentsTest.PurelyStatic
27: [ OK ] ExtentsTest.PurelyStatic (0 ms)
27: [ RUN ] ExtentsTest.RankNought
27: [ OK ] ExtentsTest.RankNought (0 ms)
27: [ RUN ] ExtentsTest.Assignment
27: [ OK ] ExtentsTest.Assignment (0 ms)
27: [----------] 4 tests from ExtentsTest (0 ms total)
27:
27: [----------] 8 tests from MdSpanExtension
27: [ RUN ] MdSpanExtension.SlicingAllStatic
27: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
27: [ RUN ] MdSpanExtension.SlicingDynamic
27: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
27: [ RUN ] MdSpanExtension.SlicingAllStatic3D
27: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
27: [ RUN ] MdSpanExtension.SlicingEqualsView3D
27: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
27: [ RUN ] MdSpanExtension.additionWorks
27: [ OK ] MdSpanExtension.additionWorks (0 ms)
27: [ RUN ] MdSpanExtension.subtractionWorks
27: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
27: [ RUN ] MdSpanExtension.multiplicationWorks
27: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
27: [ RUN ] MdSpanExtension.divisionWorks
27: [ OK ] MdSpanExtension.divisionWorks (0 ms)
27: [----------] 8 tests from MdSpanExtension (0 ms total)
27:
27: [----------] 3 tests from LayoutTests
27: [ RUN ] LayoutTests.LayoutRightConstruction
27: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
27: [ RUN ] LayoutTests.LayoutRightProperties
27: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
27: [ RUN ] LayoutTests.LayoutRightOperator
27: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
27: [----------] 3 tests from LayoutTests (0 ms total)
27:
27: [----------] 1 test from MdSpanTest
27: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
27: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
27: [----------] 1 test from MdSpanTest (0 ms total)
27:
27: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
27: [ RUN ] MdSpanTest/0.Rank
27: [ OK ] MdSpanTest/0.Rank (0 ms)
27: [ RUN ] MdSpanTest/0.DynamicRank
27: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
27: [ RUN ] MdSpanTest/0.Extents
27: [ OK ] MdSpanTest/0.Extents (0 ms)
27: [ RUN ] MdSpanTest/0.Strides
27: [ OK ] MdSpanTest/0.Strides (0 ms)
27: [ RUN ] MdSpanTest/0.Properties
27: [ OK ] MdSpanTest/0.Properties (0 ms)
27: [ RUN ] MdSpanTest/0.Operator
27: [ OK ] MdSpanTest/0.Operator (0 ms)
27: [----------] 6 tests from MdSpanTest/0 (1 ms total)
27:
27: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
27: [ RUN ] MdSpanTest/1.Rank
27: [ OK ] MdSpanTest/1.Rank (0 ms)
27: [ RUN ] MdSpanTest/1.DynamicRank
27: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
27: [ RUN ] MdSpanTest/1.Extents
27: [ OK ] MdSpanTest/1.Extents (0 ms)
27: [ RUN ] MdSpanTest/1.Strides
27: [ OK ] MdSpanTest/1.Strides (0 ms)
27: [ RUN ] MdSpanTest/1.Properties
27: [ OK ] MdSpanTest/1.Properties (0 ms)
27: [ RUN ] MdSpanTest/1.Operator
27: [ OK ] MdSpanTest/1.Operator (0 ms)
27: [----------] 6 tests from MdSpanTest/1 (0 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 32 tests from 7 test cases ran. (2 ms total)
27: [ PASSED ] 32 tests.
27/65 Test #27: MDSpanTests ........................... Passed 0.05 sec
test 28
Start 28: MdtypesUnitTest
28: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml"
28: Test timeout computed to be: 30
28: [==========] Running 9 tests from 2 test cases.
28: [----------] Global test environment set-up.
28: [----------] 2 tests from CheckpointDataTest
28: [ RUN ] CheckpointDataTest.SingleDataTest
28: [ OK ] CheckpointDataTest.SingleDataTest (6 ms)
28: [ RUN ] CheckpointDataTest.MultiDataTest
28: [ OK ] CheckpointDataTest.MultiDataTest (38 ms)
28: [----------] 2 tests from CheckpointDataTest (44 ms total)
28:
28: [----------] 7 tests from ForceBuffers
28: [ RUN ] ForceBuffers.ConstructsUnpinned
28: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms)
28: [ RUN ] ForceBuffers.ConstructsPinned
28: [ OK ] ForceBuffers.ConstructsPinned (0 ms)
28: [ RUN ] ForceBuffers.ConstructsEmpty
28: [ OK ] ForceBuffers.ConstructsEmpty (0 ms)
28: [ RUN ] ForceBuffers.ResizeWorks
28: [ OK ] ForceBuffers.ResizeWorks (0 ms)
28: [ RUN ] ForceBuffers.PaddingWorks
28: [ OK ] ForceBuffers.PaddingWorks (0 ms)
28: [ RUN ] ForceBuffers.CopyWorks
28: [ OK ] ForceBuffers.CopyWorks (0 ms)
28: [ RUN ] ForceBuffers.CopyDoesNotPin
28: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms)
28: [----------] 7 tests from ForceBuffers (0 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 9 tests from 2 test cases ran. (46 ms total)
28: [ PASSED ] 9 tests.
28/65 Test #28: MdtypesUnitTest ....................... Passed 0.08 sec
test 29
Start 29: OnlineHelpUnitTests
29: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml"
29: Test timeout computed to be: 30
29: [==========] Running 22 tests from 4 test cases.
29: [----------] Global test environment set-up.
29: [----------] 6 tests from TextTableFormatterTest
29: [ RUN ] TextTableFormatterTest.HandlesBasicCase
29: [ OK ] TextTableFormatterTest.HandlesBasicCase (1 ms)
29: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
29: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesIndentation
29: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
29: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
29: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
29: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms)
29: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
29: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms)
29: [----------] 6 tests from TextTableFormatterTest (3 ms total)
29:
29: [----------] 3 tests from HelpManagerTest
29: [ RUN ] HelpManagerTest.HandlesRootTopic
29: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms)
29: [ RUN ] HelpManagerTest.HandlesSubTopics
29: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
29: [ RUN ] HelpManagerTest.HandlesInvalidTopics
29: [ OK ] HelpManagerTest.HandlesInvalidTopics (1 ms)
29: [----------] 3 tests from HelpManagerTest (1 ms total)
29:
29: [----------] 2 tests from HelpTopicFormattingTest
29: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
29: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms)
29: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
29: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
29: [----------] 2 tests from HelpTopicFormattingTest (1 ms total)
29:
29: [----------] 11 tests from HelpWriterContextTest
29: [ RUN ] HelpWriterContextTest.FormatsParagraphs
29: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
29: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms)
29: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
29: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralText
29: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
29: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
29: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsBulletList
29: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
29: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
29: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms)
29: [ RUN ] HelpWriterContextTest.FormatsGridTable
29: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms)
29: [ RUN ] HelpWriterContextTest.FormatsTitles
29: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
29: [----------] 11 tests from HelpWriterContextTest (3 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 22 tests from 4 test cases ran. (8 ms total)
29: [ PASSED ] 22 tests.
29/65 Test #29: OnlineHelpUnitTests ................... Passed 0.05 sec
test 30
Start 30: OptionsUnitTests
30: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml"
30: Test timeout computed to be: 30
30: [==========] Running 111 tests from 18 test cases.
30: [----------] Global test environment set-up.
30: [----------] 5 tests from AbstractOptionStorageTest
30: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
30: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
30: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
30: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms)
30: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
30: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms)
30: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
30: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (1 ms)
30: [----------] 5 tests from AbstractOptionStorageTest (2 ms total)
30:
30: [----------] 10 tests from FileNameOptionTest
30: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
30: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
30: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
30: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
30: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
30: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
30: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension
30: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms)
30: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue
30: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms)
30: [----------] 10 tests from FileNameOptionTest (0 ms total)
30:
30: [----------] 15 tests from FileNameOptionManagerTest
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
30: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
30: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
30: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
30: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
30: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
30: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
30: [----------] 15 tests from FileNameOptionManagerTest (1 ms total)
30:
30: [----------] 1 test from OptionsTest
30: [ RUN ] OptionsTest.FailsOnNonsafeStorage
30: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
30: [----------] 1 test from OptionsTest (0 ms total)
30:
30: [----------] 9 tests from OptionsAssignerTest
30: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
30: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
30: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
30: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
30: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMissingValue
30: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesExtraValue
30: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesGroups
30: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesSections
30: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
30: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
30: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
30: [----------] 9 tests from OptionsAssignerTest (0 ms total)
30:
30: [----------] 4 tests from OptionsAssignerBooleanTest
30: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
30: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
30: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
30: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
30: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
30: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (1 ms)
30: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
30:
30: [----------] 13 tests from OptionsAssignerIntegerTest
30: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
30: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
30: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
30: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
30: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
30: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
30: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
30: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
30: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
30: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total)
30:
30: [----------] 5 tests from OptionsAssignerDoubleTest
30: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
30: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
30: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (1 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
30: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
30: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
30: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total)
30:
30: [----------] 9 tests from OptionsAssignerStringTest
30: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
30: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
30: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
30: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
30: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
30: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
30: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
30: [----------] 9 tests from OptionsAssignerStringTest (0 ms total)
30:
30: [----------] 6 tests from OptionsAssignerEnumTest
30: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
30: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
30: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
30: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
30: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
30: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
30: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total)
30:
30: [----------] 8 tests from RepeatingOptionSectionTest
30: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
30: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
30: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
30: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (1 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
30: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
30: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
30: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
30: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
30: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
30: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
30: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total)
30:
30: [----------] 1 test from TimeUnitManagerTest
30: [ RUN ] TimeUnitManagerTest.BasicOperations
30: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
30: [----------] 1 test from TimeUnitManagerTest (0 ms total)
30:
30: [----------] 4 tests from TimeUnitBehaviorTest
30: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
30: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
30: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
30: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
30: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
30: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
30: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total)
30:
30: [----------] 2 tests from TreeValueSupportAssignTest
30: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
30: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
30: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
30: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
30: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
30:
30: [----------] 1 test from TreeValueSupportAssignErrorTest
30: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
30: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
30: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
30:
30: [----------] 5 tests from TreeValueSupportCheckTest
30: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
30: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
30: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
30: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
30: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
30: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
30: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
30: [----------] 5 tests from TreeValueSupportCheckTest (1 ms total)
30:
30: [----------] 6 tests from TreeValueSupportAdjustTest
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
30: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (1 ms)
30: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
30: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
30: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms)
30: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
30: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms)
30: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total)
30:
30: [----------] 7 tests from TreeValueSupportTest
30: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
30: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
30: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsInt64Option
30: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsStringOption
30: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsFloatOption
30: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms)
30: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
30: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms)
30: [ RUN ] TreeValueSupportTest.SupportsEnumOption
30: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms)
30: [----------] 7 tests from TreeValueSupportTest (2 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 111 tests from 18 test cases ran. (11 ms total)
30: [ PASSED ] 111 tests.
30/65 Test #30: OptionsUnitTests ...................... Passed 0.05 sec
test 31
Start 31: PbcutilUnitTest
31: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml"
31: Test timeout computed to be: 30
31: [==========] Running 33 tests from 5 test cases.
31: [----------] Global test environment set-up.
31: [----------] 1 test from ShiftTest
31: [ RUN ] ShiftTest.CoordinateShiftWorks
31: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms)
31: [----------] 1 test from ShiftTest (0 ms total)
31:
31: [----------] 2 tests from MShift
31: [ RUN ] MShift.shiftsAndUnshifts
31: [ OK ] MShift.shiftsAndUnshifts (0 ms)
31: [ RUN ] MShift.shiftsAndUnshiftsSelf
31: [ OK ] MShift.shiftsAndUnshiftsSelf (1 ms)
31: [----------] 2 tests from MShift (1 ms total)
31:
31: [----------] 1 test from PbcTest
31: [ RUN ] PbcTest.CalcShiftsWorks
31: [ OK ] PbcTest.CalcShiftsWorks (1 ms)
31: [----------] 1 test from PbcTest (1 ms total)
31:
31: [----------] 2 tests from PbcEnumsTest
31: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
31: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
31: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
31: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
31: [----------] 2 tests from PbcEnumsTest (0 ms total)
31:
31: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (1 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms)
31: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26
31: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (1 ms)
31: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (17 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 33 tests from 5 test cases ran. (19 ms total)
31: [ PASSED ] 33 tests.
31/65 Test #31: PbcutilUnitTest ....................... Passed 0.05 sec
test 32
Start 32: RandomUnitTests
32: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RandomUnitTests.xml"
32: Test timeout computed to be: 30
32: [==========] Running 44 tests from 10 test cases.
32: [----------] Global test environment set-up.
32: [----------] 4 tests from ExponentialDistributionTest
32: [ RUN ] ExponentialDistributionTest.Output
32: [ OK ] ExponentialDistributionTest.Output (1 ms)
32: [ RUN ] ExponentialDistributionTest.Logical
32: [ OK ] ExponentialDistributionTest.Logical (0 ms)
32: [ RUN ] ExponentialDistributionTest.Reset
32: [ OK ] ExponentialDistributionTest.Reset (0 ms)
32: [ RUN ] ExponentialDistributionTest.AltParam
32: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from ExponentialDistributionTest (1 ms total)
32:
32: [----------] 4 tests from GammaDistributionTest
32: [ RUN ] GammaDistributionTest.Output
32: [ OK ] GammaDistributionTest.Output (1 ms)
32: [ RUN ] GammaDistributionTest.Logical
32: [ OK ] GammaDistributionTest.Logical (0 ms)
32: [ RUN ] GammaDistributionTest.Reset
32: [ OK ] GammaDistributionTest.Reset (0 ms)
32: [ RUN ] GammaDistributionTest.AltParam
32: [ OK ] GammaDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from GammaDistributionTest (1 ms total)
32:
32: [----------] 4 tests from NormalDistributionTest
32: [ RUN ] NormalDistributionTest.Output
32: [ OK ] NormalDistributionTest.Output (0 ms)
32: [ RUN ] NormalDistributionTest.Logical
32: [ OK ] NormalDistributionTest.Logical (0 ms)
32: [ RUN ] NormalDistributionTest.Reset
32: [ OK ] NormalDistributionTest.Reset (0 ms)
32: [ RUN ] NormalDistributionTest.AltParam
32: [ OK ] NormalDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from NormalDistributionTest (0 ms total)
32:
32: [----------] 1 test from SeedTest
32: [ RUN ] SeedTest.makeRandomSeed
32: [ OK ] SeedTest.makeRandomSeed (0 ms)
32: [----------] 1 test from SeedTest (1 ms total)
32:
32: [----------] 6 tests from TabulatedNormalDistributionTest
32: [ RUN ] TabulatedNormalDistributionTest.Output14
32: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Output16
32: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
32: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Logical
32: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.Reset
32: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
32: [ RUN ] TabulatedNormalDistributionTest.AltParam
32: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
32: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total)
32:
32: [----------] 1 test from TabulatedNormalDistributionTableTest
32: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
32: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (4 ms)
32: [----------] 1 test from TabulatedNormalDistributionTableTest (4 ms total)
32:
32: [----------] 6 tests from ThreeFry2x64Test
32: [ RUN ] ThreeFry2x64Test.Logical
32: [ OK ] ThreeFry2x64Test.Logical (0 ms)
32: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
32: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms)
32: [ RUN ] ThreeFry2x64Test.Reseed
32: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
32: [ RUN ] ThreeFry2x64Test.Discard
32: [ OK ] ThreeFry2x64Test.Discard (0 ms)
32: [ RUN ] ThreeFry2x64Test.InvalidCounter
32: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
32: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
32: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
32: [----------] 6 tests from ThreeFry2x64Test (1 ms total)
32:
32: [----------] 4 tests from UniformIntDistributionTest
32: [ RUN ] UniformIntDistributionTest.Output
32: [ OK ] UniformIntDistributionTest.Output (0 ms)
32: [ RUN ] UniformIntDistributionTest.Logical
32: [ OK ] UniformIntDistributionTest.Logical (0 ms)
32: [ RUN ] UniformIntDistributionTest.Reset
32: [ OK ] UniformIntDistributionTest.Reset (0 ms)
32: [ RUN ] UniformIntDistributionTest.AltParam
32: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
32: [----------] 4 tests from UniformIntDistributionTest (0 ms total)
32:
32: [----------] 5 tests from UniformRealDistributionTest
32: [ RUN ] UniformRealDistributionTest.GenerateCanonical
32: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms)
32: [ RUN ] UniformRealDistributionTest.Output
32: [ OK ] UniformRealDistributionTest.Output (1 ms)
32: [ RUN ] UniformRealDistributionTest.Logical
32: [ OK ] UniformRealDistributionTest.Logical (0 ms)
32: [ RUN ] UniformRealDistributionTest.Reset
32: [ OK ] UniformRealDistributionTest.Reset (0 ms)
32: [ RUN ] UniformRealDistributionTest.AltParam
32: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
32: [----------] 5 tests from UniformRealDistributionTest (1 ms total)
32:
32: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (1 ms)
32: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
32: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
32: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (2 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 44 tests from 10 test cases ran. (12 ms total)
32: [ PASSED ] 44 tests.
32/65 Test #32: RandomUnitTests ....................... Passed 0.07 sec
test 33
Start 33: RestraintTests
33: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RestraintTests.xml"
33: Test timeout computed to be: 30
33: [==========] Running 1 test from 1 test case.
33: [----------] Global test environment set-up.
33: [----------] 1 test from RestraintManager
33: [ RUN ] RestraintManager.restraintList
33: [ OK ] RestraintManager.restraintList (1 ms)
33: [----------] 1 test from RestraintManager (1 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 1 test from 1 test case ran. (1 ms total)
33: [ PASSED ] 1 test.
33/65 Test #33: RestraintTests ........................ Passed 0.04 sec
test 34
Start 34: TableUnitTests
34: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TableUnitTests.xml"
34: Test timeout computed to be: 30
34: [==========] Running 16 tests from 2 test cases.
34: [----------] Global test environment set-up.
34: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
34: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
34: [ OK ] SplineTableTest/0.HandlesIncorrectInput (2 ms)
34: [ RUN ] SplineTableTest/0.Sinc
34: [ OK ] SplineTableTest/0.Sinc (2 ms)
34: [ RUN ] SplineTableTest/0.LJ12
34: [ OK ] SplineTableTest/0.LJ12 (43 ms)
34: [ RUN ] SplineTableTest/0.PmeCorrection
34: [ OK ] SplineTableTest/0.PmeCorrection (2 ms)
34: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
34: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms)
34: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
34: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (2 ms)
34: [ RUN ] SplineTableTest/0.TwoFunctions
34: [ OK ] SplineTableTest/0.TwoFunctions (108 ms)
34: [ RUN ] SplineTableTest/0.ThreeFunctions
34: [ OK ] SplineTableTest/0.ThreeFunctions (131 ms)
34: [----------] 8 tests from SplineTableTest/0 (291 ms total)
34:
34: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
34: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
34: [ OK ] SplineTableTest/1.HandlesIncorrectInput (2 ms)
34: [ RUN ] SplineTableTest/1.Sinc
34: [ OK ] SplineTableTest/1.Sinc (3 ms)
34: [ RUN ] SplineTableTest/1.LJ12
34: [ OK ] SplineTableTest/1.LJ12 (108 ms)
34: [ RUN ] SplineTableTest/1.PmeCorrection
34: [ OK ] SplineTableTest/1.PmeCorrection (3 ms)
34: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
34: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms)
34: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
34: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms)
34: [ RUN ] SplineTableTest/1.TwoFunctions
34: [ OK ] SplineTableTest/1.TwoFunctions (243 ms)
34: [ RUN ] SplineTableTest/1.ThreeFunctions
34: [ OK ] SplineTableTest/1.ThreeFunctions (330 ms)
34: [----------] 8 tests from SplineTableTest/1 (692 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 16 tests from 2 test cases ran. (984 ms total)
34: [ PASSED ] 16 tests.
34/65 Test #34: TableUnitTests ........................ Passed 1.02 sec
test 35
Start 35: TaskAssignmentUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 3 tests from 2 test cases.
35: [----------] Global test environment set-up.
35: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
35: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
35: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms)
35: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
35: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
35: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total)
35:
35: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
35: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
35: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (1 ms)
35: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (1 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 3 tests from 2 test cases ran. (3 ms total)
35: [ PASSED ] 3 tests.
35/65 Test #35: TaskAssignmentUnitTests ............... Passed 0.04 sec
test 36
Start 36: TopologyTest
36: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TopologyTest.xml"
36: Test timeout computed to be: 30
36: [==========] Running 31 tests from 5 test cases.
36: [----------] Global test environment set-up.
36: [----------] 3 tests from ExclusionBlockTest
36: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
36: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
36: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
36: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
36: [ RUN ] ExclusionBlockTest.MergeExclusions
36: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
36: [----------] 3 tests from ExclusionBlockTest (0 ms total)
36:
36: [----------] 6 tests from InteractionListTest
36: [ RUN ] InteractionListTest.EmptyWorks
36: [ OK ] InteractionListTest.EmptyWorks (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionArray
36: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms
36: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms)
36: [ RUN ] InteractionListTest.CanAddInteractionPointer
36: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms)
36: [ RUN ] InteractionListTest.CanAddListToOtherList
36: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms)
36: [ RUN ] InteractionListTest.ClearingWorks
36: [ OK ] InteractionListTest.ClearingWorks (0 ms)
36: [----------] 6 tests from InteractionListTest (1 ms total)
36:
36: [----------] 3 tests from MtopTest
36: [ RUN ] MtopTest.RangeBasedLoop
36: [ OK ] MtopTest.RangeBasedLoop (0 ms)
36: [ RUN ] MtopTest.Operators
36: [ OK ] MtopTest.Operators (0 ms)
36: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms
36: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms)
36: [----------] 3 tests from MtopTest (0 ms total)
36:
36: [----------] 13 tests from StringTableTest
36: [ RUN ] StringTableTest.AddSingleEntry
36: [ OK ] StringTableTest.AddSingleEntry (1 ms)
36: [ RUN ] StringTableTest.CanAccessWithAt
36: [ OK ] StringTableTest.CanAccessWithAt (1 ms)
36: [ RUN ] StringTableTest.CanAccessWithBracket
36: [ OK ] StringTableTest.CanAccessWithBracket (1 ms)
36: [ RUN ] StringTableTest.ThrowsOutOfRange
36: [ OK ] StringTableTest.ThrowsOutOfRange (1 ms)
36: [ RUN ] StringTableTest.StringCompareIsCorrect
36: [ OK ] StringTableTest.StringCompareIsCorrect (1 ms)
36: [ RUN ] StringTableTest.AddTwoDistinctEntries
36: [ OK ] StringTableTest.AddTwoDistinctEntries (1 ms)
36: [ RUN ] StringTableTest.TryToAddDuplicates
36: [ OK ] StringTableTest.TryToAddDuplicates (0 ms)
36: [ RUN ] StringTableTest.AddLargeNumberOfEntries
36: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms)
36: [ RUN ] StringTableTest.NoDuplicatesInLargeTable
36: [ OK ] StringTableTest.NoDuplicatesInLargeTable (1 ms)
36: [ RUN ] StringTableTest.CanWriteToBuffer
36: [ OK ] StringTableTest.CanWriteToBuffer (0 ms)
36: [ RUN ] StringTableTest.Roundtrip
36: [ OK ] StringTableTest.Roundtrip (0 ms)
36: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices
36: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms)
36: [ RUN ] StringTableTest.CanCopyToLegacyTable
36: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms)
36: [----------] 13 tests from StringTableTest (9 ms total)
36:
36: [----------] 6 tests from LegacySymtabTest
36: [ RUN ] LegacySymtabTest.EmptyOnOpen
36: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms)
36: [ RUN ] LegacySymtabTest.AddSingleEntry
36: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms)
36: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries
36: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms)
36: [ RUN ] LegacySymtabTest.TryToAddDuplicates
36: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms)
36: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries
36: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms)
36: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable
36: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (1 ms)
36: [----------] 6 tests from LegacySymtabTest (1 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 31 tests from 5 test cases ran. (11 ms total)
36: [ PASSED ] 31 tests.
36/65 Test #36: TopologyTest .......................... Passed 0.05 sec
test 37
Start 37: PullTest
37: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PullTest.xml"
37: Test timeout computed to be: 30
37: [==========] Running 5 tests from 1 test case.
37: [----------] Global test environment set-up.
37: [----------] 5 tests from PullTest
37: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
37: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
37: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
37: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
37: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
37: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
37: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
37: [----------] 5 tests from PullTest (0 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 5 tests from 1 test case ran. (1 ms total)
37: [ PASSED ] 5 tests.
37/65 Test #37: PullTest .............................. Passed 0.04 sec
test 38
Start 38: SimdUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SimdUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 86 tests from 3 test cases.
38: [----------] Global test environment set-up.
38: [----------] 41 tests from SimdScalarTest
38: [ RUN ] SimdScalarTest.load
38: [ OK ] SimdScalarTest.load (0 ms)
38: [ RUN ] SimdScalarTest.loadU
38: [ OK ] SimdScalarTest.loadU (0 ms)
38: [ RUN ] SimdScalarTest.store
38: [ OK ] SimdScalarTest.store (0 ms)
38: [ RUN ] SimdScalarTest.storeU
38: [ OK ] SimdScalarTest.storeU (0 ms)
38: [ RUN ] SimdScalarTest.setZero
38: [ OK ] SimdScalarTest.setZero (0 ms)
38: [ RUN ] SimdScalarTest.andNot
38: [ OK ] SimdScalarTest.andNot (0 ms)
38: [ RUN ] SimdScalarTest.fma
38: [ OK ] SimdScalarTest.fma (0 ms)
38: [ RUN ] SimdScalarTest.fms
38: [ OK ] SimdScalarTest.fms (0 ms)
38: [ RUN ] SimdScalarTest.fnma
38: [ OK ] SimdScalarTest.fnma (0 ms)
38: [ RUN ] SimdScalarTest.fnms
38: [ OK ] SimdScalarTest.fnms (0 ms)
38: [ RUN ] SimdScalarTest.maskAdd
38: [ OK ] SimdScalarTest.maskAdd (0 ms)
38: [ RUN ] SimdScalarTest.maskzMul
38: [ OK ] SimdScalarTest.maskzMul (0 ms)
38: [ RUN ] SimdScalarTest.maskzFma
38: [ OK ] SimdScalarTest.maskzFma (0 ms)
38: [ RUN ] SimdScalarTest.abs
38: [ OK ] SimdScalarTest.abs (0 ms)
38: [ RUN ] SimdScalarTest.max
38: [ OK ] SimdScalarTest.max (0 ms)
38: [ RUN ] SimdScalarTest.min
38: [ OK ] SimdScalarTest.min (0 ms)
38: [ RUN ] SimdScalarTest.round
38: [ OK ] SimdScalarTest.round (0 ms)
38: [ RUN ] SimdScalarTest.trunc
38: [ OK ] SimdScalarTest.trunc (0 ms)
38: [ RUN ] SimdScalarTest.reduce
38: [ OK ] SimdScalarTest.reduce (0 ms)
38: [ RUN ] SimdScalarTest.testBits
38: [ OK ] SimdScalarTest.testBits (0 ms)
38: [ RUN ] SimdScalarTest.anyTrue
38: [ OK ] SimdScalarTest.anyTrue (0 ms)
38: [ RUN ] SimdScalarTest.selectByMask
38: [ OK ] SimdScalarTest.selectByMask (0 ms)
38: [ RUN ] SimdScalarTest.selectByNotMask
38: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
38: [ RUN ] SimdScalarTest.blend
38: [ OK ] SimdScalarTest.blend (0 ms)
38: [ RUN ] SimdScalarTest.cvtR2I
38: [ OK ] SimdScalarTest.cvtR2I (0 ms)
38: [ RUN ] SimdScalarTest.cvttR2I
38: [ OK ] SimdScalarTest.cvttR2I (0 ms)
38: [ RUN ] SimdScalarTest.cvtI2R
38: [ OK ] SimdScalarTest.cvtI2R (0 ms)
38: [ RUN ] SimdScalarTest.cvtF2D
38: [ OK ] SimdScalarTest.cvtF2D (0 ms)
38: [ RUN ] SimdScalarTest.cvtD2D
38: [ OK ] SimdScalarTest.cvtD2D (0 ms)
38: [ RUN ] SimdScalarTest.loadI
38: [ OK ] SimdScalarTest.loadI (0 ms)
38: [ RUN ] SimdScalarTest.loadUI
38: [ OK ] SimdScalarTest.loadUI (0 ms)
38: [ RUN ] SimdScalarTest.storeI
38: [ OK ] SimdScalarTest.storeI (0 ms)
38: [ RUN ] SimdScalarTest.storeUI
38: [ OK ] SimdScalarTest.storeUI (0 ms)
38: [ RUN ] SimdScalarTest.andNotI
38: [ OK ] SimdScalarTest.andNotI (0 ms)
38: [ RUN ] SimdScalarTest.testBitsI
38: [ OK ] SimdScalarTest.testBitsI (0 ms)
38: [ RUN ] SimdScalarTest.selectByMaskI
38: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
38: [ RUN ] SimdScalarTest.selectByNotMaskI
38: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
38: [ RUN ] SimdScalarTest.blendI
38: [ OK ] SimdScalarTest.blendI (0 ms)
38: [ RUN ] SimdScalarTest.cvtB2IB
38: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
38: [ RUN ] SimdScalarTest.cvtIB2B
38: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
38: [ RUN ] SimdScalarTest.expandScalarsToTriplets
38: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
38: [----------] 41 tests from SimdScalarTest (2 ms total)
38:
38: [----------] 8 tests from SimdScalarUtilTest
38: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
38: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
38: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
38: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
38: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
38: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
38: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
38: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
38: [----------] 8 tests from SimdScalarUtilTest (0 ms total)
38:
38: [----------] 37 tests from SimdScalarMathTest
38: [ RUN ] SimdScalarMathTest.copysign
38: [ OK ] SimdScalarMathTest.copysign (0 ms)
38: [ RUN ] SimdScalarMathTest.invsqrtPair
38: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
38: [ RUN ] SimdScalarMathTest.inv
38: [ OK ] SimdScalarMathTest.inv (0 ms)
38: [ RUN ] SimdScalarMathTest.maskzInvsqrt
38: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
38: [ RUN ] SimdScalarMathTest.log
38: [ OK ] SimdScalarMathTest.log (0 ms)
38: [ RUN ] SimdScalarMathTest.exp2
38: [ OK ] SimdScalarMathTest.exp2 (0 ms)
38: [ RUN ] SimdScalarMathTest.exp
38: [ OK ] SimdScalarMathTest.exp (0 ms)
38: [ RUN ] SimdScalarMathTest.erf
38: [ OK ] SimdScalarMathTest.erf (0 ms)
38: [ RUN ] SimdScalarMathTest.erfc
38: [ OK ] SimdScalarMathTest.erfc (0 ms)
38: [ RUN ] SimdScalarMathTest.sincos
38: [ OK ] SimdScalarMathTest.sincos (0 ms)
38: [ RUN ] SimdScalarMathTest.sin
38: [ OK ] SimdScalarMathTest.sin (0 ms)
38: [ RUN ] SimdScalarMathTest.cos
38: [ OK ] SimdScalarMathTest.cos (0 ms)
38: [ RUN ] SimdScalarMathTest.tan
38: [ OK ] SimdScalarMathTest.tan (0 ms)
38: [ RUN ] SimdScalarMathTest.asin
38: [ OK ] SimdScalarMathTest.asin (0 ms)
38: [ RUN ] SimdScalarMathTest.acos
38: [ OK ] SimdScalarMathTest.acos (0 ms)
38: [ RUN ] SimdScalarMathTest.atan
38: [ OK ] SimdScalarMathTest.atan (0 ms)
38: [ RUN ] SimdScalarMathTest.atan2
38: [ OK ] SimdScalarMathTest.atan2 (0 ms)
38: [ RUN ] SimdScalarMathTest.pmeForceCorrection
38: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
38: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
38: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
38: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
38: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.invSingleAccuracy
38: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
38: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.logSingleAccuracy
38: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
38: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.expSingleAccuracy
38: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
38: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
38: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
38: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
38: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
38: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
38: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
38: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
38: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
38: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
38: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
38: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
38: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
38: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
38: [----------] 37 tests from SimdScalarMathTest (1 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 86 tests from 3 test cases ran. (3 ms total)
38: [ PASSED ] 86 tests.
38/65 Test #38: SimdUnitTests ......................... Passed 0.05 sec
test 39
Start 39: CompatibilityHelpersTests
39: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 9 tests from 6 test cases.
39: [----------] Global test environment set-up.
39: [----------] 4 tests from TemplateMPTest
39: [ RUN ] TemplateMPTest.MpWithIndexInt
39: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexIntBad
39: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexBool
39: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms)
39: [ RUN ] TemplateMPTest.MpWithIndexEnum
39: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms)
39: [----------] 4 tests from TemplateMPTest (0 ms total)
39:
39: [----------] 1 test from NotNullConstruction
39: [ RUN ] NotNullConstruction.Works
39: [ OK ] NotNullConstruction.Works (0 ms)
39: [----------] 1 test from NotNullConstruction (0 ms total)
39:
39: [----------] 1 test from NotNullCasting
39: [ RUN ] NotNullCasting.Works
39: [ OK ] NotNullCasting.Works (0 ms)
39: [----------] 1 test from NotNullCasting (0 ms total)
39:
39: [----------] 1 test from NotNullAssignment
39: [ RUN ] NotNullAssignment.Works
39: [ OK ] NotNullAssignment.Works (0 ms)
39: [----------] 1 test from NotNullAssignment (0 ms total)
39:
39: [----------] 1 test from MakeNotNull
39: [ RUN ] MakeNotNull.Works
39: [ OK ] MakeNotNull.Works (0 ms)
39: [----------] 1 test from MakeNotNull (0 ms total)
39:
39: [----------] 1 test from NotNull
39: [ RUN ] NotNull.WorksInContainers
39: [ OK ] NotNull.WorksInContainers (0 ms)
39: [----------] 1 test from NotNull (0 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 9 tests from 6 test cases ran. (1 ms total)
39: [ PASSED ] 9 tests.
39/65 Test #39: CompatibilityHelpersTests ............. Passed 0.04 sec
test 40
Start 40: GmxAnaTest
40: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxAnaTest.xml"
40: Test timeout computed to be: 600
40: [==========] Running 27 tests from 5 test cases.
40: [----------] Global test environment set-up.
40: [----------] 5 tests from Entropy
40: [ RUN ] Entropy.Schlitter_300_NoLinear
40: [ OK ] Entropy.Schlitter_300_NoLinear (1 ms)
40: [ RUN ] Entropy.Schlitter_300_Linear
40: [ OK ] Entropy.Schlitter_300_Linear (0 ms)
40: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
40: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms)
40: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
40: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms)
40: [ RUN ] Entropy.QuasiHarmonic_200_Linear
40: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms)
40: [----------] 5 tests from Entropy (2 ms total)
40:
40: [----------] 10 tests from MindistTest
40: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistWorksWithSingleAtoms (4 ms)
40: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 2: 'atom3'
40: Selected 3: 'atoms12'
40: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (3 ms)
40: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistDoesNotPickUpContacts (4 ms)
40: [ RUN ] MindistTest.mindistPicksUpContacts
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.mindistPicksUpContacts (3 ms)
40: [ RUN ] MindistTest.ngWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.ngWorks (4 ms)
40: [ RUN ] MindistTest.groupWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 3: 'atoms12'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.groupWorks (3 ms)
40: [ RUN ] MindistTest.maxDistWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 2: 'atom3'
40: Selected 3: 'atoms12'
40: [ OK ] MindistTest.maxDistWorks (3 ms)
40: [ RUN ] MindistTest.noPbcWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 0: 'atom1'
40: Selected 1: 'atom2'
40: [ OK ] MindistTest.noPbcWorks (3 ms)
40: [ RUN ] MindistTest.resPerTimeWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 3: 'atoms12'
40: Selected 2: 'atom3'
40: [ OK ] MindistTest.resPerTimeWorks (2 ms)
40: [ RUN ] MindistTest.matrixWorks
40: Group 0 ( atom1) has 1 elements
40: Group 1 ( atom2) has 1 elements
40: Group 2 ( atom3) has 1 elements
40: Group 3 ( atoms12) has 2 elements
40: Group 4 ( atoms23) has 2 elements
40: Group 5 ( atoms123) has 3 elements
40: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40: Selected 5: 'atoms123'
40: Special case: making distance matrix between all atoms in group atoms123
40: [ OK ] MindistTest.matrixWorks (3 ms)
40: [----------] 10 tests from MindistTest (33 ms total)
40:
40: [----------] 3 tests from MsdTest
40: [ RUN ] MsdTest.threeDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.threeDimensionalDiffusion (2 ms)
40: [ RUN ] MsdTest.twoDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.twoDimensionalDiffusion (2 ms)
40: [ RUN ] MsdTest.oneDimensionalDiffusion
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( particles) has 3 elements
40: There is one group in the index
40:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
40:
40: Used 1 restart points spaced 200 ps over 9 ps
40:
40: Fitting from 1 to 8 ps
40:
40: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
40: [ OK ] MsdTest.oneDimensionalDiffusion (2 ms)
40: [----------] 3 tests from MsdTest (7 ms total)
40:
40: [----------] 3 tests from MsdMolTest
40: [ RUN ] MsdMolTest.diffMolMassWeighted
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( water) has 15 elements
40: There is one group in the index
40: Split group of 15 atoms into 5 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -838860833
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted_msdmol.xvg
40: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolMassWeighted (2825 ms)
40: [ RUN ] MsdMolTest.diffMolNonMassWeighted
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( water) has 15 elements
40: There is one group in the index
40: Split group of 15 atoms into 5 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -295974121
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted_msdmol.xvg
40: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolNonMassWeighted (2887 ms)
40: [ RUN ] MsdMolTest.diffMolSelected
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Generating 1-4 interactions: fudge = 0.5
40: Number of degrees of freedom in T-Coupling group rest is 27.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Calculating diffusion coefficients for molecules.
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
40:
40: Select a group to calculate mean squared displacement for:
40: Group 0 ( mol) has 9 elements
40: There is one group in the index
40: Split group of 9 atoms into 3 molecules
40: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
40:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
40:
40: Used 1 restart points spaced 200 ps over 0.1 ps
40:
40: Setting the LD random seed to -4266019
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40:
40: Generated 330891 of the 330891 1-4 parameter combinations
40:
40: Excluding 2 bonded neighbours molecule type 'SOL'
40:
40: This run will generate roughly 0 Mb of data
40: Wrote per-molecule output to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected_msdmol.xvg
40: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
40: Fitting from 0.008 to 0.088 ps
40:
40: D[ mol] 7.8614 (+/- 1.5619) 1e-5 cm^2/s
40: [ OK ] MsdMolTest.diffMolSelected (2580 ms)
40: [----------] 3 tests from MsdMolTest (8292 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: trr version: GMX_trn_file (single precision)
40:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (5 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (6 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (5 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (5 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
40: Group 0 ( System) has 6 elements
40: Group 1 ( Water) has 6 elements
40: Group 2 ( SOL) has 6 elements
40: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
40: Selected 0: 'System'
40: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (4 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (30 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 27 tests from 5 test cases ran. (8365 ms total)
40: [ PASSED ] 27 tests.
40/65 Test #40: GmxAnaTest ............................ Passed 8.41 sec
test 41
Start 41: GmxPreprocessTests
41: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml"
41: Test timeout computed to be: 1920
41: [==========] Running 51 tests from 9 test cases.
41: [----------] Global test environment set-up.
41: [----------] 4 tests from GenconfTest
41: [ RUN ] GenconfTest.nbox_Works
41: [ OK ] GenconfTest.nbox_Works (2 ms)
41: [ RUN ] GenconfTest.nbox_norenumber_Works
41: [ OK ] GenconfTest.nbox_norenumber_Works (1 ms)
41: [ RUN ] GenconfTest.nbox_dist_Works
41: [ OK ] GenconfTest.nbox_dist_Works (2 ms)
41: [ RUN ] GenconfTest.nbox_rot_Works
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: center of geometry: 1.733667, 1.477000, 0.905167
41: [ OK ] GenconfTest.nbox_rot_Works (2 ms)
41: [----------] 4 tests from GenconfTest (9 ms total)
41:
41: [----------] 2 tests from GenionTest
41: [ RUN ] GenionTest.HighConcentrationIonPlacement
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
41: buffer. The cluster pair list does have a buffering effect, but choosing
41: a larger rlist might be necessary for good energy conservation.
41:
41:
41: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: Generating 1-4 interactions: fudge = 0.5
41: Number of degrees of freedom in T-Coupling group rest is 1308.00
41:
41: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
41: You are using a plain Coulomb cut-off, which might produce artifacts.
41: You might want to consider using PME electrostatics.
41:
41:
41:
41: There were 3 notes
41: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
41: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
41: Group 0 ( System) has 653 elements
41: Group 1 ( Water) has 648 elements
41: Group 2 ( SOL) has 648 elements
41: Group 3 ( non-Water) has 5 elements
41: Group 4 ( Other) has 5 elements
41: Group 5 ( METH) has 5 elements
41: Select a group: Number of (3-atomic) solvent molecules: 216
41: Using random seed 1997.
41: Replacing solvent molecule 56 (atom 168) with NA
41: Replacing solvent molecule 120 (atom 360) with NA
41: Replacing solvent molecule 182 (atom 546) with NA
41: Replacing solvent molecule 71 (atom 213) with NA
41: Replacing solvent molecule 189 (atom 567) with CL
41: Replacing solvent molecule 54 (atom 162) with CL
41: Replacing solvent molecule 155 (atom 465) with CL
41: Replacing solvent molecule 99 (atom 297) with CL
41:
41: Setting the LD random seed to -603980099
41:
41: Generated 331705 of the 331705 non-bonded parameter combinations
41:
41: Generated 331705 of the 331705 1-4 parameter combinations
41:
41: Excluding 2 bonded neighbours molecule type 'SOL'
41:
41: Excluding 3 bonded neighbours molecule type 'methane'
41: Analysing residue names:
41: There are: 216 Water residues
41: There are: 1 Other residues
41: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
41:
41: This run will generate roughly 0 Mb of data
41: Will try to add 4 NA ions and 4 CL ions.
41: Select a continuous group of solvent molecules
41: Selected 1: 'Water'
41: [ OK ] GenionTest.HighConcentrationIonPlacement (2719 ms)
41: [ RUN ] GenionTest.NoIonPlacement
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
41: buffer. The cluster pair list does have a buffering effect, but choosing
41: a larger rlist might be necessary for good energy conservation.
41:
41:
41: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: Generating 1-4 interactions: fudge = 0.5
41: Number of degrees of freedom in T-Coupling group rest is 1308.00
41:
41: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
41: You are using a plain Coulomb cut-off, which might produce artifacts.
41: You might want to consider using PME electrostatics.
41:
41:
41:
41: There were 3 notes
41: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
41: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
41: No ions to add, will just copy input configuration.
41: Setting the LD random seed to 2145582939
41:
41: Generated 331705 of the 331705 non-bonded parameter combinations
41:
41: Generated 331705 of the 331705 1-4 parameter combinations
41:
41: Excluding 2 bonded neighbours molecule type 'SOL'
41:
41: Excluding 3 bonded neighbours molecule type 'methane'
41: Analysing residue names:
41: There are: 216 Water residues
41: There are: 1 Other residues
41: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
41:
41: This run will generate roughly 0 Mb of data
41: [ OK ] GenionTest.NoIonPlacement (2520 ms)
41: [----------] 2 tests from GenionTest (5239 ms total)
41:
41: [----------] 1 test from GenRestrTest
41: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
41:
41: Reading structure file
41: Group 0 ( System) has 156 elements
41: Group 1 ( Protein) has 156 elements
41: Group 2 ( Protein-H) has 75 elements
41: Group 3 ( C-alpha) has 10 elements
41: Group 4 ( Backbone) has 30 elements
41: Group 5 ( MainChain) has 40 elements
41: Group 6 ( MainChain+Cb) has 49 elements
41: Group 7 ( MainChain+H) has 52 elements
41: Group 8 ( SideChain) has 104 elements
41: Group 9 ( SideChain-H) has 35 elements
41: Select a group: Select group to position restrain
41: Selected 3: 'C-alpha'
41: [ OK ] GenRestrTest.SimpleRestraintsGenerated (6 ms)
41: [----------] 1 test from GenRestrTest (6 ms total)
41:
41: [----------] 9 tests from PreprocessingAtomTypesTest
41: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
41: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
41: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
41: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
41: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
41: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
41: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
41: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
41: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
41: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
41: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
41: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total)
41:
41: [----------] 10 tests from PreprocessingBondAtomTypeTest
41: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
41: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
41: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
41: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
41: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
41: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
41: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
41: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
41: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
41: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
41: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
41: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
41: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total)
41:
41: [----------] 5 tests from InsertMoleculesTest
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 8 atoms)!
41:
41: Added 1 molecules (out of 1 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
41:
41: Output configuration contains 8 atoms in 4 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (5 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 2 atoms)!
41:
Try 2 success (now 4 atoms)!
41:
Try 3 success (now 6 atoms)!
41:
Try 4 success (now 8 atoms)!
41:
Try 5 success (now 10 atoms)!
41:
41: Added 5 molecules (out of 5 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
41:
41: Output configuration contains 10 atoms in 10 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (4 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 8 atoms)!
41:
Try 2 success (now 10 atoms)!
41:
41: Added 2 molecules (out of 2 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
41:
41: Output configuration contains 10 atoms in 4 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (4 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
41: Reading solute configuration
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41:
Try 1 success (now 650 atoms)!
41:
Try 2 success (now 652 atoms)!
41:
Try 3 success (now 654 atoms)!
41:
Try 4 success (now 656 atoms)!
41:
41: Added 4 molecules (out of 4 requested)
41: Replaced 8 residues (24 atoms)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
41:
41: Output configuration contains 632 atoms in 212 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (21 ms)
41: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Using random seed 1997
41: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
41:
41:
Try 1 success (now 2 atoms)!
41:
Try 2 success (now 4 atoms)!
41:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
41:
Try 13 success (now 6 atoms)!
41:
41: Added 3 molecules (out of 4 requested)
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
41:
41: Output configuration contains 6 atoms in 3 residues
41: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (5 ms)
41: [----------] 5 tests from InsertMoleculesTest (39 ms total)
41:
41: [----------] 14 tests from GetIrTest
41: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
41: Ignoring obsolete mdp entry 'title'
41: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (11 ms)
41: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
41: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (15 ms)
41: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsKeyWithoutValue (8 ms)
41: [ RUN ] GetIrTest.RejectsValueWithoutKey
41: [ OK ] GetIrTest.RejectsValueWithoutKey (15 ms)
41: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
41: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (15 ms)
41: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (8 ms)
41: [ RUN ] GetIrTest.AcceptsEmptyLines
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsEmptyLines (7 ms)
41: [ RUN ] GetIrTest.AcceptsElectricField
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricField (8 ms)
41: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (8 ms)
41: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (7 ms)
41: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
41: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (7 ms)
41: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsImplicitSolventNo (7 ms)
41: [ RUN ] GetIrTest.RejectsImplicitSolventYes
41: [ OK ] GetIrTest.RejectsImplicitSolventYes (15 ms)
41: [ RUN ] GetIrTest.AcceptsMimic
41:
41: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
41: For a correct single-point energy evaluation with nsteps = 0, use
41: continuation = yes to avoid constraining the input coordinates.
41:
41: [ OK ] GetIrTest.AcceptsMimic (8 ms)
41: [----------] 14 tests from GetIrTest (140 ms total)
41:
41: [----------] 5 tests from SolvateTest
41: [ RUN ] SolvateTest.cs_box_Works
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 1x1x1 boxes
41: Solvent box contains 270 atoms in 90 residues
41: Removed 129 solvent atoms due to solvent-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 47 residues
41: Generated solvent containing 141 atoms in 47 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
41:
41: Output configuration contains 141 atoms in 47 residues
41: Volume : 1.331 (nm^3)
41: Density : 1056.36 (g/l)
41: Number of solvent molecules: 47
41:
41: [ OK ] SolvateTest.cs_box_Works (25 ms)
41: [ RUN ] SolvateTest.cs_cp_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 886 residues
41: Generated solvent containing 2658 atoms in 886 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
41:
41: Output configuration contains 2664 atoms in 888 residues
41: Volume : 27.2709 (nm^3)
41: Density : 974.777 (g/l)
41: Number of solvent molecules: 886
41:
41: [ OK ] SolvateTest.cs_cp_Works (152 ms)
41: [ RUN ] SolvateTest.cs_cp_p_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 886 residues
41: Generated solvent containing 2658 atoms in 886 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
41:
41: Output configuration contains 2664 atoms in 888 residues
41: Volume : 27.2709 (nm^3)
41: Density : 974.777 (g/l)
41: Number of solvent molecules: 886
41:
41: Processing topology
41: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
41: [ OK ] SolvateTest.cs_cp_p_Works (147 ms)
41: [ RUN ] SolvateTest.shell_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 2x2x2 boxes
41: Solvent box contains 3660 atoms in 1220 residues
41: Removed 987 solvent atoms due to solvent-solvent overlap
41: Removed 1902 solvent atoms more than 1.000000 nm from solute.
41: Removed 15 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 1 molecule type:
41: SOL ( 3 atoms): 252 residues
41: Generated solvent containing 756 atoms in 252 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
41:
41: Output configuration contains 762 atoms in 254 residues
41: Volume : 27.2709 (nm^3)
41: Density : 279.3 (g/l)
41: Number of solvent molecules: 252
41:
41: [ OK ] SolvateTest.shell_Works (84 ms)
41: [ RUN ] SolvateTest.update_Topology_Works
41: Reading solute configuration
41: Reading solvent configuration
41:
41: Initialising inter-atomic distances...
41:
41: WARNING: Masses and atomic (Van der Waals) radii will be guessed
41: based on residue and atom names, since they could not be
41: definitively assigned from the information in your input
41: files. These guessed numbers might deviate from the mass
41: and radius of the atom type. Please check the output
41: files if necessary.
41:
41: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
41: from the source below. This means the results may be different
41: compared to previous GROMACS versions.
41:
41: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
41: A. Bondi
41: van der Waals Volumes and Radii
41: J. Phys. Chem. 68 (1964) pp. 441-451
41: -------- -------- --- Thank You --- -------- --------
41:
41: Generating solvent configuration
41: Will generate new solvent configuration of 3x3x3 boxes
41: Solvent box contains 14952 atoms in 4984 residues
41: Removed 2787 solvent atoms due to solvent-solvent overlap
41: Removed 30 solvent atoms due to solute-solvent overlap
41: Sorting configuration
41: Found 2 different molecule types:
41: HOH ( 3 atoms): 1876 residues
41: SOL ( 3 atoms): 2169 residues
41: Generated solvent containing 0 atoms in 0 residues
41: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
41:
41: Output configuration contains 12141 atoms in 4047 residues
41: Volume : 125 (nm^3)
41: Density : 968.963 (g/l)
41: Number of solvent molecules: 4045
41:
41: Processing topology
41: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
41: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
41: [ OK ] SolvateTest.update_Topology_Works (601 ms)
41: [----------] 5 tests from SolvateTest (1009 ms total)
41:
41: [----------] 1 test from TopDirTests
41: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
41: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
41: [----------] 1 test from TopDirTests (0 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 51 tests from 9 test cases ran. (6443 ms total)
41: [ PASSED ] 51 tests.
41/65 Test #41: GmxPreprocessTests .................... Passed 6.48 sec
test 42
Start 42: Pdb2gmx1Test
42: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml"
42: Test timeout computed to be: 1920
42: [==========] Running 24 tests from 1 test case.
42: [----------] Global test environment set-up.
42: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (352 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (398 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (330 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (327 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (330 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (384 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (379 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip3p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (353 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (324 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (381 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (303 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (320 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (384 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (402 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (392 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip4p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (356 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 0 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (292 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 0 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (404 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 0 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (362 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 0 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (295 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 25 donors and 23 acceptors were found.
42: There are 41 hydrogen bonds
42: Will use HISE for residue 8
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS3 HIS8
42: SG9 NE251
42: HIS8 NE251 1.055
42: MET12 SD83 0.763 0.990
42: Marked 124 virtual sites
42: Added 16 dummy masses
42: Added 26 new constraints
42: Before cleaning: 653 pairs
42: Before cleaning: 663 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
42: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 128
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (128 atoms, 16 residues)
42:
42: Identified residue ALA2 as a starting terminus.
42:
42: Identified residue SER17 as a ending terminus.
42: Start terminus ALA-2: NH3+
42: End terminus SER-17: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 252 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 254, now 254
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 663 dihedrals, 51 impropers, 457 angles
42: 650 pairs, 254 bonds and 130 virtual sites
42:
42: Total mass 1846.112 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (376 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 30 donors and 22 acceptors were found.
42: There are 36 hydrogen bonds
42: Will use HISE for residue 29
42: Will use HISE for residue 32
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: CYS27 HIS29
42: SG90 NE2111
42: HIS29 NE2111 0.987
42: HIS32 NE2135 1.590 1.155
42: Marked 132 virtual sites
42: Added 10 dummy masses
42: Added 19 new constraints
42: Before cleaning: 748 pairs
42: Before cleaning: 778 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
42: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 149
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (149 atoms, 16 residues)
42:
42: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue THR18 as a starting terminus.
42:
42: Identified residue PHE33 as a ending terminus.
42: Start terminus THR-18: NH3+
42: End terminus PHE-33: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 281 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 290, now 290
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 778 dihedrals, 72 impropers, 516 angles
42: 736 pairs, 290 bonds and 133 virtual sites
42:
42: Total mass 2088.357 a.m.u.
42:
42: Total charge 1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (370 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 22 acceptors were found.
42: There are 26 hydrogen bonds
42: Will use HISE for residue 45
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS45
42: NE295
42: MET46 SD102 1.078
42: Marked 123 virtual sites
42: Added 22 dummy masses
42: Added 35 new constraints
42: Before cleaning: 676 pairs
42: Before cleaning: 696 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
42: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 132
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (132 atoms, 16 residues)
42:
42: Identified residue ALA34 as a starting terminus.
42:
42: Identified residue ALA49 as a ending terminus.
42: Start terminus ALA-34: NH3+
42: End terminus ALA-49: COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 255 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 261, now 261
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 696 dihedrals, 56 impropers, 472 angles
42: 667 pairs, 261 bonds and 132 virtual sites
42:
42: Total mass 1861.128 a.m.u.
42:
42: Total charge -1.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (374 ms)
42: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
42: All occupancies are one
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
42: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
42: Analysing hydrogen-bonding network for automated assignment of histidine
42: protonation. 22 donors and 21 acceptors were found.
42: There are 30 hydrogen bonds
42: Will use HISE for residue 60
42: 8 out of 8 lines of specbond.dat converted successfully
42: Special Atom Distance matrix:
42: HIS60
42: NE285
42: CYS62 SG98 0.803
42: Marked 111 virtual sites
42: Added 18 dummy masses
42: Added 31 new constraints
42: Before cleaning: 603 pairs
42: Before cleaning: 618 dihedrals
42: Keeping all generated dihedrals
42: Using the Oplsaa force field in directory oplsaa.ff
42:
42: going to rename oplsaa.ff/aminoacids.r2b
42: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
42: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
42:
42: Analyzing pdb file
42: Splitting chemical chains based on TER records or chain id changing.
42:
42: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
42:
42: chain #res #atoms
42:
42: 1 ' ' 16 117
42:
42: All occupancies are one
42:
42: Reading residue database... (Oplsaa)
42:
42: Processing chain 1 (117 atoms, 16 residues)
42:
42: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
42:
42: Identified residue LYS50 as a starting terminus.
42:
42: Identified residue PRO65 as a ending terminus.
42: Start terminus LYS-50: NH3+
42: End terminus PRO-65: PRO-COO-
42:
42: Checking for duplicate atoms....
42:
42: Generating any missing hydrogen atoms and/or adding termini.
42:
42: Now there are 16 residues with 228 atoms
42:
42: Making bonds...
42:
42: Number of bonds was 232, now 232
42:
42: Generating angles, dihedrals and pairs...
42:
42: Making cmap torsions...
42:
42: There are 618 dihedrals, 48 impropers, 419 angles
42: 597 pairs, 232 bonds and 116 virtual sites
42:
42: Total mass 1662.883 a.m.u.
42:
42: Total charge 0.000 e
42:
42: Writing topology
42:
42: Writing coordinate file...
42:
42: --------- PLEASE NOTE ------------
42:
42: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
42:
42: The Oplsaa force field and the tip5p water model are used.
42:
42: --------- ETON ESAELP ------------
42: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (345 ms)
42: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (8539 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 24 tests from 1 test case ran. (8539 ms total)
42: [ PASSED ] 24 tests.
42/65 Test #42: Pdb2gmx1Test .......................... Passed 8.58 sec
test 43
Start 43: Pdb2gmx2Test
43: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml"
43: Test timeout computed to be: 1920
43: [==========] Running 32 tests from 2 test cases.
43: [----------] Global test environment set-up.
43: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (197 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (183 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (157 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (143 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 37 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 37 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (184 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 53 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 51 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (223 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 36 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 36 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (182 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 33 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 31 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (206 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (157 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (188 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (159 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (165 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 37 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 305 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 165 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 172, now 167
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 77 impropers, 241 angles
43: 267 pairs, 167 bonds and 37 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (162 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 53 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 429 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 202 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 216, now 211
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 134 impropers, 316 angles
43: 273 pairs, 211 bonds and 51 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (231 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 36 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 349 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 168 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 179, now 174
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 102 impropers, 260 angles
43: 242 pairs, 174 bonds and 36 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (217 ms)
43: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 33 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 299 dihedrals
43: Using the Gromos43a1 force field in directory gromos43a1.ff
43:
43: going to rename gromos43a1.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos43a1)
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 150 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 159, now 154
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 80 impropers, 227 angles
43: 232 pairs, 154 bonds and 31 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos43a1 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (153 ms)
43: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (2917 ms total)
43:
43: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (167 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (246 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (169 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (157 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 39 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 39 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (196 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 57 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 55 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (204 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 38 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 38 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (175 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 35 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 33 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spc water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (163 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 0 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (191 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 0 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (230 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 0 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (190 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 0 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (158 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 25 donors and 23 acceptors were found.
43: There are 41 hydrogen bonds
43: Will use HISE for residue 8
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS3 HIS8
43: SG9 NE251
43: HIS8 NE251 1.055
43: MET12 SD83 0.763 0.990
43: Marked 39 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 267 pairs
43: Before cleaning: 312 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
43: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 128
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (128 atoms, 16 residues)
43:
43: Identified residue ALA2 as a starting terminus.
43:
43: Identified residue SER17 as a ending terminus.
43: Start terminus ALA-2: NH3+
43: End terminus SER-17: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 167 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 174, now 169
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 90 dihedrals, 79 impropers, 245 angles
43: 267 pairs, 169 bonds and 39 virtual sites
43:
43: Total mass 1846.116 a.m.u.
43:
43: Total charge 0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (195 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 30 donors and 22 acceptors were found.
43: There are 36 hydrogen bonds
43: Will use HISE for residue 29
43: Will use HISE for residue 32
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: CYS27 HIS29
43: SG90 NE2111
43: HIS29 NE2111 0.987
43: HIS32 NE2135 1.590 1.155
43: Marked 57 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 273 pairs
43: Before cleaning: 443 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
43: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 149
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (149 atoms, 16 residues)
43:
43: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue THR18 as a starting terminus.
43:
43: Identified residue PHE33 as a ending terminus.
43: Start terminus THR-18: NH3+
43: End terminus PHE-33: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 206 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 220, now 215
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 93 dihedrals, 138 impropers, 324 angles
43: 273 pairs, 215 bonds and 55 virtual sites
43:
43: Total mass 2088.361 a.m.u.
43:
43: Total charge 1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (260 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 22 acceptors were found.
43: There are 26 hydrogen bonds
43: Will use HISE for residue 45
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS45
43: NE295
43: MET46 SD102 1.078
43: Marked 38 virtual sites
43: Added 4 dummy masses
43: Added 8 new constraints
43:
43: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 242 pairs
43: Before cleaning: 356 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
43: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 132
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (132 atoms, 16 residues)
43:
43: Identified residue ALA34 as a starting terminus.
43:
43: Identified residue ALA49 as a ending terminus.
43: Start terminus ALA-34: NH3+
43: End terminus ALA-49: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 170 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 181, now 176
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 81 dihedrals, 104 impropers, 264 angles
43: 242 pairs, 176 bonds and 38 virtual sites
43:
43: Total mass 1861.132 a.m.u.
43:
43: Total charge -1.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (221 ms)
43: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
43: All occupancies are one
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
43: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
43: Analysing hydrogen-bonding network for automated assignment of histidine
43: protonation. 22 donors and 21 acceptors were found.
43: There are 30 hydrogen bonds
43: Will use HISE for residue 60
43: 8 out of 8 lines of specbond.dat converted successfully
43: Special Atom Distance matrix:
43: HIS60
43: NE285
43: CYS62 SG98 0.803
43: Marked 35 virtual sites
43: Added 4 dummy masses
43: Added 10 new constraints
43:
43: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom H used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43:
43: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
43: to an entry in the topology database, but the atom O used in
43: an interaction of type angle in that entry is not found in the
43: input file. Perhaps your atom and/or residue naming needs to be
43: fixed.
43:
43:
43: Before cleaning: 232 pairs
43: Before cleaning: 306 dihedrals
43: Using the Gromos53a6 force field in directory gromos53a6.ff
43:
43: going to rename gromos53a6.ff/aminoacids.r2b
43: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
43: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
43:
43: Analyzing pdb file
43: Splitting chemical chains based on TER records or chain id changing.
43:
43: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
43:
43: chain #res #atoms
43:
43: 1 ' ' 16 117
43:
43: All occupancies are one
43:
43: Reading residue database... (Gromos53a6)
43:
43: Using default: not generating all possible dihedrals
43:
43: Using default: excluding 3 bonded neighbors
43:
43: Using default: generating 1,4 H--H interactions
43:
43: Using default: removing proper dihedrals found on the same bond as a proper dihedral
43:
43: Processing chain 1 (117 atoms, 16 residues)
43:
43: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
43:
43: Identified residue LYS50 as a starting terminus.
43:
43: Identified residue PRO65 as a ending terminus.
43: Start terminus LYS-50: NH3+
43: End terminus PRO-65: COO-
43:
43: Checking for duplicate atoms....
43:
43: Generating any missing hydrogen atoms and/or adding termini.
43:
43: Now there are 16 residues with 152 atoms
43:
43: Making bonds...
43:
43: Number of bonds was 161, now 156
43:
43: Generating angles, dihedrals and pairs...
43:
43: Making cmap torsions...
43:
43: There are 78 dihedrals, 82 impropers, 231 angles
43: 232 pairs, 156 bonds and 33 virtual sites
43:
43: Total mass 1662.887 a.m.u.
43:
43: Total charge -0.000 e
43:
43: Writing topology
43:
43: Writing coordinate file...
43:
43: --------- PLEASE NOTE ------------
43:
43: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
43:
43: The Gromos53a6 force field and the spce water model are used.
43:
43: --------- ETON ESAELP ------------
43: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (163 ms)
43: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (3087 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 32 tests from 2 test cases ran. (6004 ms total)
43: [ PASSED ] 32 tests.
43/65 Test #43: Pdb2gmx2Test .......................... Passed 6.05 sec
test 44
Start 44: Pdb2gmx3Test
44: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml"
44: Test timeout computed to be: 1920
44: [==========] Running 33 tests from 6 test cases.
44: [----------] Global test environment set-up.
44: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 653 pairs
44: Before cleaning: 691 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 255, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 691 dihedrals, 51 impropers, 457 angles
44: 650 pairs, 254 bonds and 0 virtual sites
44:
44: Total mass 1846.132 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (232 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 748 pairs
44: Before cleaning: 788 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 291, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 788 dihedrals, 72 impropers, 516 angles
44: 736 pairs, 290 bonds and 0 virtual sites
44:
44: Total mass 2088.366 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (285 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 676 pairs
44: Before cleaning: 727 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 262, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 727 dihedrals, 56 impropers, 472 angles
44: 667 pairs, 261 bonds and 0 virtual sites
44:
44: Total mass 1861.124 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (259 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Before cleaning: 603 pairs
44: Before cleaning: 634 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 233, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 634 dihedrals, 48 impropers, 419 angles
44: 597 pairs, 232 bonds and 0 virtual sites
44:
44: Total mass 1662.888 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (277 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 124 virtual sites
44: Added 16 dummy masses
44: Added 26 new constraints
44: Before cleaning: 653 pairs
44: Before cleaning: 691 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 255, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 691 dihedrals, 51 impropers, 457 angles
44: 650 pairs, 254 bonds and 130 virtual sites
44:
44: Total mass 1846.132 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (250 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 132 virtual sites
44: Added 10 dummy masses
44: Added 19 new constraints
44: Before cleaning: 748 pairs
44: Before cleaning: 788 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 291, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 788 dihedrals, 72 impropers, 516 angles
44: 736 pairs, 290 bonds and 133 virtual sites
44:
44: Total mass 2088.366 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (310 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 123 virtual sites
44: Added 22 dummy masses
44: Added 35 new constraints
44: Before cleaning: 676 pairs
44: Before cleaning: 727 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 262, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 727 dihedrals, 56 impropers, 472 angles
44: 667 pairs, 261 bonds and 132 virtual sites
44:
44: Total mass 1861.124 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (273 ms)
44: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Marked 111 virtual sites
44: Added 18 dummy masses
44: Added 31 new constraints
44: Before cleaning: 603 pairs
44: Before cleaning: 634 dihedrals
44: Keeping all generated dihedrals
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 233, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 634 dihedrals, 48 impropers, 419 angles
44: 597 pairs, 232 bonds and 116 virtual sites
44:
44: Total mass 1662.888 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Amber99sb-ildn force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (223 ms)
44: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (2111 ms total)
44:
44: [----------] 1 test from ForAmber99sb_ildnWithTip4p/Pdb2gmxTest
44: [ RUN ] ForAmber99sb_ildnWithTip4p/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
44: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
44:
44: going to rename amber99sb-ildn.ff/aminoacids.r2b
44:
44: going to rename amber99sb-ildn.ff/dna.r2b
44:
44: going to rename amber99sb-ildn.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/tip4p.pdb...
44: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 2 4 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Amber99sb-ildn)
44:
44: Processing chain 1 (4 atoms, 2 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 2 residues with 8 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 4, now 4
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 2 angles
44: 0 pairs, 4 bonds and 0 virtual sites
44:
44: Total mass 36.032 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/tip4p.pdb.
44:
44: The Amber99sb-ildn force field and the tip4p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForAmber99sb_ildnWithTip4p/Pdb2gmxTest.ProducesMatchingTopology/0 (66 ms)
44: [----------] 1 test from ForAmber99sb_ildnWithTip4p/Pdb2gmxTest (66 ms total)
44:
44: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 653 pairs
44: Before cleaning: 663 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 254, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 663 dihedrals, 48 impropers, 457 angles
44: 650 pairs, 254 bonds and 0 virtual sites
44:
44: Total mass 1846.115 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (253 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 748 pairs
44: Before cleaning: 778 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus PHE-33: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 290, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 778 dihedrals, 49 impropers, 516 angles
44: 736 pairs, 290 bonds and 0 virtual sites
44:
44: Total mass 2088.361 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (287 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 676 pairs
44: Before cleaning: 696 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44: Start terminus ALA-34: NH3+
44: End terminus ALA-49: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 261, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 696 dihedrals, 39 impropers, 472 angles
44: 667 pairs, 261 bonds and 0 virtual sites
44:
44: Total mass 1861.130 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (271 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 603 pairs
44: Before cleaning: 618 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44: Start terminus LYS-50: NH3+
44: End terminus PRO-65: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 232, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 618 dihedrals, 38 impropers, 419 angles
44: 597 pairs, 232 bonds and 0 virtual sites
44:
44: Total mass 1662.885 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (201 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 124 virtual sites
44: Added 16 dummy masses
44: Added 26 new constraints
44: Before cleaning: 653 pairs
44: Before cleaning: 663 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 128
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (128 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 252 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 254, now 254
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 663 dihedrals, 48 impropers, 457 angles
44: 650 pairs, 254 bonds and 130 virtual sites
44:
44: Total mass 1846.115 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (293 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 30 donors and 22 acceptors were found.
44: There are 36 hydrogen bonds
44: Will use HISE for residue 29
44: Will use HISE for residue 32
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS27 HIS29
44: SG90 NE2111
44: HIS29 NE2111 0.987
44: HIS32 NE2135 1.590 1.155
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 132 virtual sites
44: Added 10 dummy masses
44: Added 19 new constraints
44: Before cleaning: 748 pairs
44: Before cleaning: 778 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
44: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 149
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (149 atoms, 16 residues)
44:
44: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue PHE33 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus PHE-33: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 281 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 290, now 290
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 778 dihedrals, 49 impropers, 516 angles
44: 736 pairs, 290 bonds and 133 virtual sites
44:
44: Total mass 2088.361 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (289 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 22 acceptors were found.
44: There are 26 hydrogen bonds
44: Will use HISE for residue 45
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS45
44: NE295
44: MET46 SD102 1.078
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 123 virtual sites
44: Added 22 dummy masses
44: Added 35 new constraints
44: Before cleaning: 676 pairs
44: Before cleaning: 696 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
44: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 132
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (132 atoms, 16 residues)
44:
44: Identified residue ALA34 as a starting terminus.
44:
44: Identified residue ALA49 as a ending terminus.
44: Start terminus ALA-34: NH3+
44: End terminus ALA-49: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 261, now 261
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 696 dihedrals, 39 impropers, 472 angles
44: 667 pairs, 261 bonds and 132 virtual sites
44:
44: Total mass 1861.130 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (268 ms)
44: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 22 donors and 21 acceptors were found.
44: There are 30 hydrogen bonds
44: Will use HISE for residue 60
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS60
44: NE285
44: CYS62 SG98 0.803
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Marked 111 virtual sites
44: Added 18 dummy masses
44: Added 31 new constraints
44: Before cleaning: 603 pairs
44: Before cleaning: 618 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
44: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
44:
44: chain #res #atoms
44:
44: 1 ' ' 16 117
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 (117 atoms, 16 residues)
44:
44: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need.
44:
44: Identified residue LYS50 as a starting terminus.
44:
44: Identified residue PRO65 as a ending terminus.
44: Start terminus LYS-50: NH3+
44: End terminus PRO-65: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 228 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 232, now 232
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 14 cmap torsion pairs
44:
44: There are 618 dihedrals, 38 impropers, 419 angles
44: 597 pairs, 232 bonds and 116 virtual sites
44:
44: Total mass 1662.885 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (235 ms)
44: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (2097 ms total)
44:
44: [----------] 8 tests from ChainSep/Pdb2gmxTest
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 651 pairs
44: Before cleaning: 661 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44: Start terminus PHE-6: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 258 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 258, now 258
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 10 cmap torsion pairs
44:
44: There are 661 dihedrals, 46 impropers, 463 angles
44: 648 pairs, 258 bonds and 0 virtual sites
44:
44: Total mass 1882.146 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (230 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 123 pairs
44: Before cleaning: 123 dihedrals
44: Keeping all generated dihedrals
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 10 donors and 7 acceptors were found.
44: There are 7 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: HIS8
44: NE223
44: MET12 SD55 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 317 pairs
44: Before cleaning: 322 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 4 28
44:
44: 2 'B' 7 58
44:
44: 3 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (28 atoms, 4 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 51 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 50, now 50
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 123 dihedrals, 9 impropers, 88 angles
44: 123 pairs, 50 bonds and 0 virtual sites
44:
44: Total mass 434.421 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (58 atoms, 7 residues)
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus PHE-6: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 7 residues with 124 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 125, now 125
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 5 cmap torsion pairs
44:
44: There are 322 dihedrals, 19 impropers, 227 angles
44: 314 pairs, 125 bonds and 0 virtual sites
44:
44: Total mass 846.083 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 51 atoms 4 residues
44:
44: Including chain 2 in system: 124 atoms 7 residues
44:
44: Including chain 3 in system: 83 atoms 5 residues
44:
44: Now there are 258 atoms and 16 residues
44:
44: Total mass in system 1882.146 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (164 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 651 pairs
44: Before cleaning: 661 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ILE-9: COO-
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 258 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 258, now 258
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 10 cmap torsion pairs
44:
44: There are 661 dihedrals, 46 impropers, 463 angles
44: 648 pairs, 258 bonds and 0 virtual sites
44:
44: Total mass 1882.146 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (240 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 10 donors and 12 acceptors were found.
44: There are 13 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3
44: SG9
44: HIS8 NE251 1.055
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 288 pairs
44: Before cleaning: 293 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 152 pairs
44: Before cleaning: 152 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 8 61
44:
44: 2 'B' 3 25
44:
44: 3 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (61 atoms, 8 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ILE-9: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 8 residues with 114 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 115, now 115
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6 cmap torsion pairs
44:
44: There are 293 dihedrals, 23 impropers, 203 angles
44: 285 pairs, 115 bonds and 0 virtual sites
44:
44: Total mass 888.952 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (25 atoms, 3 residues)
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 61 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 60, now 60
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 152 dihedrals, 5 impropers, 112 angles
44: 152 pairs, 60 bonds and 0 virtual sites
44:
44: Total mass 391.552 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 114 atoms 8 residues
44:
44: Including chain 2 in system: 61 atoms 3 residues
44:
44: Including chain 3 in system: 83 atoms 5 residues
44:
44: Now there are 258 atoms and 16 residues
44:
44: Total mass in system 1882.146 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (164 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 650 pairs
44: Before cleaning: 660 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Merged chains into joint molecule definitions at 3 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44: Start terminus PHE-6: NH3+
44: End terminus ILE-9: COO-
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 261 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 260, now 260
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 8 cmap torsion pairs
44:
44: There are 660 dihedrals, 45 impropers, 466 angles
44: 647 pairs, 260 bonds and 0 virtual sites
44:
44: Total mass 1900.162 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (265 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 123 pairs
44: Before cleaning: 123 dihedrals
44: Keeping all generated dihedrals
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 6 donors and 4 acceptors were found.
44: There are 3 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 164 pairs
44: Before cleaning: 169 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 152 pairs
44: Before cleaning: 152 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 4 28
44:
44: 2 'B' 4 33
44:
44: 3 'B' 3 25
44:
44: 4 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (28 atoms, 4 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue GLU5 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus GLU-5: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 51 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 50, now 50
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 123 dihedrals, 9 impropers, 88 angles
44: 123 pairs, 50 bonds and 0 virtual sites
44:
44: Total mass 434.421 a.m.u.
44:
44: Total charge -2.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (33 atoms, 4 residues)
44:
44: Identified residue PHE6 as a starting terminus.
44:
44: Identified residue ILE9 as a ending terminus.
44: Start terminus PHE-6: NH3+
44: End terminus ILE-9: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 4 residues with 66 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 67, now 67
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 2 cmap torsion pairs
44:
44: There are 169 dihedrals, 13 impropers, 118 angles
44: 161 pairs, 67 bonds and 0 virtual sites
44:
44: Total mass 472.547 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'B' (25 atoms, 3 residues)
44:
44: Identified residue LYS10 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus LYS-10: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 61 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 60, now 60
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 152 dihedrals, 5 impropers, 112 angles
44: 152 pairs, 60 bonds and 0 virtual sites
44:
44: Total mass 391.552 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Processing chain 4 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 51 atoms 4 residues
44:
44: Including chain 2 in system: 66 atoms 4 residues
44:
44: Including chain 3 in system: 61 atoms 3 residues
44:
44: Including chain 4 in system: 83 atoms 5 residues
44:
44: Now there are 261 atoms and 16 residues
44:
44: Total mass in system 1900.162 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (165 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 25 donors and 23 acceptors were found.
44: There are 41 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 652 pairs
44: Before cleaning: 662 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: Merged chains into joint molecule definitions at 1 places.
44:
44: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 16 127
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (127 atoms, 16 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus MET-12: COO-
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 255 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 256, now 256
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 12 cmap torsion pairs
44:
44: There are 662 dihedrals, 47 impropers, 460 angles
44: 649 pairs, 256 bonds and 0 virtual sites
44:
44: Total mass 1864.131 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (231 ms)
44: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: Analysing hydrogen-bonding network for automated assignment of histidine
44: protonation. 14 donors and 15 acceptors were found.
44: There are 20 hydrogen bonds
44: Will use HISE for residue 8
44: 8 out of 8 lines of specbond.dat converted successfully
44: Special Atom Distance matrix:
44: CYS3 HIS8
44: SG9 NE251
44: HIS8 NE251 1.055
44: MET12 SD83 0.763 0.990
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 441 pairs
44: Before cleaning: 446 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 211 pairs
44: Before cleaning: 216 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
44: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 11 86
44:
44: 2 'C' 5 41
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (86 atoms, 11 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue MET12 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus MET-12: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 11 residues with 172 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 173, now 173
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 9 cmap torsion pairs
44:
44: There are 446 dihedrals, 29 impropers, 312 angles
44: 438 pairs, 173 bonds and 0 virtual sites
44:
44: Total mass 1262.488 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'C' (41 atoms, 5 residues)
44:
44: Identified residue ASN13 as a starting terminus.
44:
44: Identified residue SER17 as a ending terminus.
44: Start terminus ASN-13: NH3+
44: End terminus SER-17: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 5 residues with 83 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 83, now 83
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 3 cmap torsion pairs
44:
44: There are 216 dihedrals, 18 impropers, 148 angles
44: 211 pairs, 83 bonds and 0 virtual sites
44:
44: Total mass 601.643 a.m.u.
44:
44: Total charge 1.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 172 atoms 11 residues
44:
44: Including chain 2 in system: 83 atoms 5 residues
44:
44: Now there are 255 atoms and 16 residues
44:
44: Total mass in system 1864.131 a.m.u.
44:
44: Total charge in system 0.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (164 ms)
44: [----------] 8 tests from ChainSep/Pdb2gmxTest (1623 ms total)
44:
44: [----------] 4 tests from ChainChanges/Pdb2gmxTest
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on changing chain id only (ignoring TER records).
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (96 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records only (ignoring chain id).
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (96 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (118 ms)
44: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 83 pairs
44: Before cleaning: 83 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 145 pairs
44: Before cleaning: 150 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
44: Read 'Fragments of peptides and ions', 47 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records and chain id changing.
44:
44: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 3 19
44:
44: 2 'B' 3 28
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (19 atoms, 3 residues)
44:
44: Identified residue ALA2 as a starting terminus.
44:
44: Identified residue ASP4 as a ending terminus.
44: Start terminus ALA-2: NH3+
44: End terminus ASP-4: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 36 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 35, now 35
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 83 dihedrals, 6 impropers, 61 angles
44: 83 pairs, 35 bonds and 0 virtual sites
44:
44: Total mass 306.314 a.m.u.
44:
44: Total charge -1.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'B' (28 atoms, 3 residues)
44:
44: Identified residue THR18 as a starting terminus.
44:
44: Identified residue TRP20 as a ending terminus.
44: Start terminus THR-18: NH3+
44: End terminus TRP-20: COO-
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 3 residues with 57 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 58, now 58
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 1 cmap torsion pairs
44:
44: There are 150 dihedrals, 5 impropers, 103 angles
44: 142 pairs, 58 bonds and 0 virtual sites
44:
44: Total mass 404.468 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Writing topology
44:
44: Including chain 1 in system: 36 atoms 3 residues
44:
44: Including chain 2 in system: 57 atoms 3 residues
44:
44: Now there are 93 atoms and 6 residues
44:
44: Total mass in system 710.782 a.m.u.
44:
44: Total charge in system -1.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (127 ms)
44: [----------] 4 tests from ChainChanges/Pdb2gmxTest (438 ms total)
44:
44: [----------] 4 tests from ForCharmm27CyclicSystem/Pdb2gmxTest
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/0
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: WARNING: all CONECT records are ignored
44: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 6040 pairs
44: Before cleaning: 6605 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 6040 pairs
44: Before cleaning: 6605 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb...
44: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
44:
44: Moved all the water blocks to the end
44:
44: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms
44:
44: chain #res #atoms
44:
44: 1 'P' 71 1527
44:
44: 2 'Q' 71 1527
44:
44: 3 'Q' 7 7
44:
44: 4 ' ' 10 10 (only water)
44:
44: 5 ' ' 16 16 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'P' (1527 atoms, 71 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 71 residues with 2297 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 2481, now 2481
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6605 dihedrals, 183 impropers, 4434 angles
44: 5827 pairs, 2481 bonds and 0 virtual sites
44:
44: Total mass 22984.514 a.m.u.
44:
44: Total charge -71.000 e
44:
44: Writing topology
44:
44: Processing chain 2 'Q' (1527 atoms, 71 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 71 residues with 2297 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: Number of bonds was 2481, now 2481
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 6605 dihedrals, 183 impropers, 4434 angles
44: 5827 pairs, 2481 bonds and 0 virtual sites
44:
44: Total mass 22984.514 a.m.u.
44:
44: Total charge -71.000 e
44:
44: Writing topology
44:
44: Processing chain 3 'Q' (7 atoms, 7 residues)
44:
44: Residue MG72 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG73 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG74 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG75 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG76 has type 'Ion', assuming it is not linked into a chain.
44:
44: Disabling further notes about ions.
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 7 residues with 7 atoms
44: Chain time...
44:
44: Making bonds...
44:
44: No bonds
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 0 angles
44: 0 pairs, 0 bonds and 0 virtual sites
44:
44: Total mass 170.135 a.m.u.
44:
44: Total charge 14.000 e
44:
44: Writing topology
44:
44: Processing chain 4 (10 atoms, 10 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 10 residues with 30 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 30, now 30
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 30 angles
44: 0 pairs, 30 bonds and 0 virtual sites
44:
44: Total mass 180.154 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Processing chain 5 (16 atoms, 16 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 48 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 48, now 48
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 48 angles
44: 0 pairs, 48 bonds and 0 virtual sites
44:
44: Total mass 288.246 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Including chain 1 in system: 2297 atoms 71 residues
44:
44: Including chain 2 in system: 2297 atoms 71 residues
44:
44: Including chain 3 in system: 7 atoms 7 residues
44:
44: Including chain 4 in system: 30 atoms 10 residues
44:
44: Including chain 5 in system: 48 atoms 16 residues
44:
44: Now there are 4679 atoms and 175 residues
44:
44: Total mass in system 46607.563 a.m.u.
44:
44: Total charge in system -128.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/0 (18734 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/1
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 2325 pairs
44: Before cleaning: 2325 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb...
44: Read 'CARNOCYCLIN-A', 413 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 60 413
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (413 atoms, 60 residues)
44:
44: Identified residue LEU1 as a starting terminus.
44:
44: Identified residue LEU60 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 60 residues with 878 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 880, now 880
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 59 cmap torsion pairs
44:
44: There are 2325 dihedrals, 137 impropers, 1614 angles
44: 2319 pairs, 880 bonds and 0 virtual sites
44:
44: Total mass 5866.087 a.m.u.
44:
44: Total charge 4.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/1 (1464 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/2
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: WARNING: all CONECT records are ignored
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 12080 pairs
44: Before cleaning: 13210 dihedrals
44: Keeping all generated dihedrals
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb...
44: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: Moved all the water blocks to the end
44:
44: Merged chains into joint molecule definitions at 2 places.
44:
44: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms
44:
44: chain #res #atoms
44:
44: 1 'P' 149 3061
44:
44: 2 ' ' 10 10 (only water)
44:
44: 3 ' ' 16 16 (only water)
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'P' (3061 atoms, 149 residues)
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Identified residue G1 as a starting terminus.
44:
44: Identified residue U71 as a ending terminus.
44:
44: Residue MG72 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG73 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG74 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG75 has type 'Ion', assuming it is not linked into a chain.
44:
44: Residue MG76 has type 'Ion', assuming it is not linked into a chain.
44:
44: Disabling further notes about ions.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 149 residues with 4601 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 4962, now 4962
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 13210 dihedrals, 366 impropers, 8868 angles
44: 11654 pairs, 4962 bonds and 0 virtual sites
44:
44: Total mass 46139.162 a.m.u.
44:
44: Total charge -128.000 e
44:
44: Writing topology
44:
44: Processing chain 2 (10 atoms, 10 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 10 residues with 30 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 30, now 30
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 30 angles
44: 0 pairs, 30 bonds and 0 virtual sites
44:
44: Total mass 180.154 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Processing chain 3 (16 atoms, 16 residues)
44:
44: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 16 residues with 48 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 48, now 48
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 0 dihedrals, 0 impropers, 48 angles
44: 0 pairs, 48 bonds and 0 virtual sites
44:
44: Total mass 288.246 a.m.u.
44:
44: Total charge 0.000 e
44:
44: Including chain 1 in system: 4601 atoms 149 residues
44:
44: Including chain 2 in system: 30 atoms 10 residues
44:
44: Including chain 3 in system: 48 atoms 16 residues
44:
44: Now there are 4679 atoms and 175 residues
44:
44: Total mass in system 46607.563 a.m.u.
44:
44: Total charge in system -128.000 e
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-rna.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/2 (38360 ms)
44: [ RUN ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/3
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
44: All occupancies are one
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
44: 8 out of 8 lines of specbond.dat converted successfully
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
44: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
44: Before cleaning: 2325 pairs
44: Before cleaning: 2325 dihedrals
44: Keeping all generated dihedrals
44: Using the Charmm27 force field in directory charmm27.ff
44:
44: going to rename charmm27.ff/aminoacids.r2b
44:
44: going to rename charmm27.ff/rna.r2b
44: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb...
44: Read 'CARNOCYCLIN-A', 413 atoms
44:
44: Analyzing pdb file
44: Splitting chemical chains based on TER records or chain id changing.
44:
44: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms
44:
44: chain #res #atoms
44:
44: 1 'A' 60 413
44:
44: All occupancies are one
44:
44: Reading residue database... (Charmm27)
44:
44: Processing chain 1 'A' (413 atoms, 60 residues)
44:
44: Identified residue LEU1 as a starting terminus.
44:
44: Identified residue LEU60 as a ending terminus.
44:
44: Checking for duplicate atoms....
44:
44: Generating any missing hydrogen atoms and/or adding termini.
44:
44: Now there are 60 residues with 878 atoms
44:
44: Making bonds...
44:
44: Number of bonds was 880, now 880
44:
44: Generating angles, dihedrals and pairs...
44:
44: Making cmap torsions...
44:
44: There are 59 cmap torsion pairs
44:
44: There are 2325 dihedrals, 137 impropers, 1614 angles
44: 2319 pairs, 880 bonds and 0 virtual sites
44:
44: Total mass 5866.087 a.m.u.
44:
44: Total charge 4.000 e
44:
44: Writing topology
44:
44: Writing coordinate file...
44:
44: --------- PLEASE NOTE ------------
44:
44: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/cyclic-protein-small.pdb.
44:
44: The Charmm27 force field and the tip3p water model are used.
44:
44: --------- ETON ESAELP ------------
44: [ OK ] ForCharmm27CyclicSystem/Pdb2gmxTest.ProducesMatchingTopology/3 (1585 ms)
44: [----------] 4 tests from ForCharmm27CyclicSystem/Pdb2gmxTest (60145 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 33 tests from 6 test cases ran. (66480 ms total)
44: [ PASSED ] 33 tests.
44/65 Test #44: Pdb2gmx3Test .......................... Passed 66.52 sec
test 45
Start 45: CorrelationsTest
45: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CorrelationsTest.xml"
45: Test timeout computed to be: 30
45: [==========] Running 21 tests from 3 test cases.
45: [----------] Global test environment set-up.
45: [----------] 10 tests from AutocorrTest
45: [ RUN ] AutocorrTest.EacNormal
45: [ OK ] AutocorrTest.EacNormal (9 ms)
45: [ RUN ] AutocorrTest.EacNoNormalize
45: [ OK ] AutocorrTest.EacNoNormalize (5 ms)
45: [ RUN ] AutocorrTest.EacCos
45: [ OK ] AutocorrTest.EacCos (8 ms)
45: [ RUN ] AutocorrTest.EacVector
45: [ OK ] AutocorrTest.EacVector (14 ms)
45: [ RUN ] AutocorrTest.EacRcross
45: [ OK ] AutocorrTest.EacRcross (4 ms)
45: [ RUN ] AutocorrTest.EacP0
45: [ OK ] AutocorrTest.EacP0 (13 ms)
45: [ RUN ] AutocorrTest.EacP1
45: [ OK ] AutocorrTest.EacP1 (13 ms)
45: [ RUN ] AutocorrTest.EacP2
45: [ OK ] AutocorrTest.EacP2 (26 ms)
45: [ RUN ] AutocorrTest.EacP3
45: [ OK ] AutocorrTest.EacP3 (11 ms)
45: [ RUN ] AutocorrTest.EacP4
45: [ OK ] AutocorrTest.EacP4 (14 ms)
45: [----------] 10 tests from AutocorrTest (121 ms total)
45:
45: [----------] 10 tests from ExpfitTest
45: [ RUN ] ExpfitTest.EffnEXP1
45: [ OK ] ExpfitTest.EffnEXP1 (1 ms)
45: [ RUN ] ExpfitTest.EffnEXP2
45: [ OK ] ExpfitTest.EffnEXP2 (3 ms)
45: [ RUN ] ExpfitTest.EffnEXPEXP
45: [ OK ] ExpfitTest.EffnEXPEXP (3 ms)
45: [ RUN ] ExpfitTest.EffnEXP5
45: [ OK ] ExpfitTest.EffnEXP5 (11 ms)
45: [ RUN ] ExpfitTest.EffnEXP7
45: [ OK ] ExpfitTest.EffnEXP7 (11 ms)
45: [ RUN ] ExpfitTest.EffnEXP9
45: [ OK ] ExpfitTest.EffnEXP9 (46 ms)
45: [ RUN ] ExpfitTest.EffnERF
45: [ OK ] ExpfitTest.EffnERF (6 ms)
45: [ RUN ] ExpfitTest.EffnERREST
45: [ OK ] ExpfitTest.EffnERREST (8 ms)
45: [ RUN ] ExpfitTest.EffnVAC
45: [ OK ] ExpfitTest.EffnVAC (19 ms)
45: [ RUN ] ExpfitTest.EffnPRES
45: [ OK ] ExpfitTest.EffnPRES (53 ms)
45: [----------] 10 tests from ExpfitTest (162 ms total)
45:
45: [----------] 1 test from ManyAutocorrelationTest
45: [ RUN ] ManyAutocorrelationTest.Empty
45: [ OK ] ManyAutocorrelationTest.Empty (0 ms)
45: [----------] 1 test from ManyAutocorrelationTest (0 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 21 tests from 3 test cases ran. (299 ms total)
45: [ PASSED ] 21 tests.
45/65 Test #45: CorrelationsTest ...................... Passed 0.33 sec
test 46
Start 46: AnalysisDataUnitTests
46: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml"
46: Test timeout computed to be: 30
46: [==========] Running 69 tests from 14 test cases.
46: [----------] Global test environment set-up.
46: [----------] 3 tests from AnalysisDataInitializationTest
46: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
46: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
46: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
46: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms)
46: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
46: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (1 ms)
46: [----------] 3 tests from AnalysisDataInitializationTest (2 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
46: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms)
46: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms)
46: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (1 ms)
46: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/0 (12 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
46: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (3 ms)
46: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (1 ms)
46: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (1 ms)
46: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (1 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/1 (13 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
46: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (3 ms)
46: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (1 ms)
46: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (1 ms)
46: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (1 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/2 (16 ms total)
46:
46: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
46: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (2 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
46: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (1 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
46: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (3 ms)
46: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
46: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (1 ms)
46: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
46: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (1 ms)
46: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
46: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (1 ms)
46: [----------] 8 tests from AnalysisDataCommonTest/3 (15 ms total)
46:
46: [----------] 4 tests from AnalysisArrayDataTest
46: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
46: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (1 ms)
46: [ RUN ] AnalysisArrayDataTest.StorageWorks
46: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms)
46: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
46: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
46: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
46: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
46: [----------] 4 tests from AnalysisArrayDataTest (3 ms total)
46:
46: [----------] 6 tests from AverageModuleTest
46: [ RUN ] AverageModuleTest.BasicTest
46: [ OK ] AverageModuleTest.BasicTest (3 ms)
46: [ RUN ] AverageModuleTest.HandlesMultipointData
46: [ OK ] AverageModuleTest.HandlesMultipointData (3 ms)
46: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
46: [ OK ] AverageModuleTest.HandlesMultipleDataSets (3 ms)
46: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
46: [ OK ] AverageModuleTest.HandlesDataSetAveraging (3 ms)
46: [ RUN ] AverageModuleTest.CanCustomizeXAxis
46: [ OK ] AverageModuleTest.CanCustomizeXAxis (2 ms)
46: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
46: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (2 ms)
46: [----------] 6 tests from AverageModuleTest (17 ms total)
46:
46: [----------] 2 tests from FrameAverageModuleTest
46: [ RUN ] FrameAverageModuleTest.BasicTest
46: [ OK ] FrameAverageModuleTest.BasicTest (2 ms)
46: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
46: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (3 ms)
46: [----------] 2 tests from FrameAverageModuleTest (5 ms total)
46:
46: [----------] 7 tests from AnalysisHistogramSettingsTest
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
46: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
46: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
46: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total)
46:
46: [----------] 2 tests from SimpleHistogramModuleTest
46: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
46: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (3 ms)
46: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
46: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (3 ms)
46: [----------] 2 tests from SimpleHistogramModuleTest (6 ms total)
46:
46: [----------] 3 tests from WeightedHistogramModuleTest
46: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
46: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (3 ms)
46: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
46: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (3 ms)
46: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
46: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (3 ms)
46: [----------] 3 tests from WeightedHistogramModuleTest (9 ms total)
46:
46: [----------] 3 tests from BinAverageModuleTest
46: [ RUN ] BinAverageModuleTest.ComputesCorrectly
46: [ OK ] BinAverageModuleTest.ComputesCorrectly (2 ms)
46: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
46: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (2 ms)
46: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
46: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (3 ms)
46: [----------] 3 tests from BinAverageModuleTest (7 ms total)
46:
46: [----------] 4 tests from AbstractAverageHistogramTest
46: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
46: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (3 ms)
46: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
46: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (3 ms)
46: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
46: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (2 ms)
46: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
46: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (3 ms)
46: [----------] 4 tests from AbstractAverageHistogramTest (11 ms total)
46:
46: [----------] 3 tests from LifetimeModuleTest
46: [ RUN ] LifetimeModuleTest.BasicTest
46: [ OK ] LifetimeModuleTest.BasicTest (2 ms)
46: [ RUN ] LifetimeModuleTest.CumulativeTest
46: [ OK ] LifetimeModuleTest.CumulativeTest (2 ms)
46: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
46: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (2 ms)
46: [----------] 3 tests from LifetimeModuleTest (6 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 69 tests from 14 test cases ran. (124 ms total)
46: [ PASSED ] 69 tests.
46/65 Test #46: AnalysisDataUnitTests ................. Passed 0.17 sec
test 47
Start 47: CoordinateIOTests
47: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml"
47: Test timeout computed to be: 30
47: [==========] Running 64 tests from 19 test cases.
47: [----------] Global test environment set-up.
47: [----------] 1 test from OutputSelectorDeathTest
47: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (17 ms)
47: [----------] 1 test from OutputSelectorDeathTest (17 ms total)
47:
47: [----------] 5 tests from TrajectoryFrameWriterTest
47: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (11 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (11 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (11 ms)
47: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (22 ms)
47: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
47: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms)
47: [----------] 5 tests from TrajectoryFrameWriterTest (56 ms total)
47:
47: [----------] 5 tests from OutputAdapterContainer
47: [ RUN ] OutputAdapterContainer.MakeEmpty
47: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
47: [ RUN ] OutputAdapterContainer.AddAdapter
47: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.RejectBadAdapter
47: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
47: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
47: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
47: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
47: [----------] 5 tests from OutputAdapterContainer (1 ms total)
47:
47: [----------] 5 tests from FlagTest
47: [ RUN ] FlagTest.CanSetSimpleFlag
47: [ OK ] FlagTest.CanSetSimpleFlag (1 ms)
47: [ RUN ] FlagTest.CanAddNewBox
47: [ OK ] FlagTest.CanAddNewBox (0 ms)
47: [ RUN ] FlagTest.SetsImplicitPrecisionChange
47: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
47: [ RUN ] FlagTest.SetsImplicitStartTimeChange
47: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
47: [ RUN ] FlagTest.SetsImplicitTimeStepChange
47: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
47: [----------] 5 tests from FlagTest (2 ms total)
47:
47: [----------] 5 tests from SetAtomsTest
47: [ RUN ] SetAtomsTest.RemovesExistingAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.RemovesExistingAtoms (11 ms)
47: [ RUN ] SetAtomsTest.AddsNewAtoms
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.AddsNewAtoms (11 ms)
47: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (12 ms)
47: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (11 ms)
47: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (11 ms)
47: [----------] 5 tests from SetAtomsTest (56 ms total)
47:
47: [----------] 2 tests from SetBothTimeTest
47: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
47: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
47: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
47: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
47: [----------] 2 tests from SetBothTimeTest (1 ms total)
47:
47: [----------] 2 tests from SetStartTimeTest
47: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
47: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
47: [ RUN ] SetStartTimeTest.WorksWithZeroStart
47: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms)
47: [----------] 2 tests from SetStartTimeTest (0 ms total)
47:
47: [----------] 1 test from SetTimeStepTest
47: [ RUN ] SetTimeStepTest.SetTimeStepWorks
47: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
47: [----------] 1 test from SetTimeStepTest (0 ms total)
47:
47: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (11 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (11 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (11 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (11 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (11 ms)
47: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (11 ms)
47: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (68 ms total)
47:
47: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (11 ms)
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (11 ms)
47: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (11 ms)
47: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (34 ms total)
47:
47: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
47: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (1 ms total)
47:
47: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (22 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (22 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (22 ms)
47: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (23 ms)
47: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (91 ms total)
47:
47: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (14 ms)
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (14 ms)
47: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (15 ms)
47: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (44 ms total)
47:
47: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
47: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (1 ms total)
47:
47: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
47: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (14 ms)
47: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (14 ms)
47: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (29 ms total)
47:
47: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
47: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
47: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
47: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
47:
47: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
47: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (15 ms)
47: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (12 ms)
47: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (27 ms total)
47:
47: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
47: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
47: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms)
47: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total)
47:
47: [----------] 4 tests from ModuleSupported/NoOptionalOutput
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (11 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (11 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (11 ms)
47: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
47:
47: WARNING: Masses and atomic (Van der Waals) radii will be guessed
47: based on residue and atom names, since they could not be
47: definitively assigned from the information in your input
47: files. These guessed numbers might deviate from the mass
47: and radius of the atom type. Please check the output
47: files if necessary.
47:
47: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (11 ms)
47: [----------] 4 tests from ModuleSupported/NoOptionalOutput (45 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 64 tests from 19 test cases ran. (481 ms total)
47: [ PASSED ] 64 tests.
47/65 Test #47: CoordinateIOTests ..................... Passed 0.52 sec
test 48
Start 48: TrajectoryAnalysisUnitTests
48: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
48: Test timeout computed to be: 1920
48: [==========] Running 82 tests from 16 test cases.
48: [----------] Global test environment set-up.
48: [----------] 11 tests from AngleModuleTest
48: [ RUN ] AngleModuleTest.ComputesSimpleAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesSimpleAngles (10 ms)
48: [ RUN ] AngleModuleTest.ComputesDihedrals
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesDihedrals (8 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorPairAngles (9 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (9 ms)
48: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (8 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (8 ms)
48: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
48: Reading frames from gro file 'Test system for different angles', 33 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (10 ms)
48: [ RUN ] AngleModuleTest.ComputesMultipleAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.ComputesMultipleAngles (9 ms)
48: [ RUN ] AngleModuleTest.HandlesDynamicSelections
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesDynamicSelections (9 ms)
48: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (8 ms)
48: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (8 ms)
48: [----------] 11 tests from AngleModuleTest (100 ms total)
48:
48: [----------] 5 tests from ClustsizeTest
48: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
48: There is one group in the index
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 24
48: cmid: 2, cmax: 4, max_size: 6
48: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
48: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (7 ms)
48: [ RUN ] ClustsizeTest.NoMolShortCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
48: There is one group in the index
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 24
48: cmid: 1, cmax: 6, max_size: 6
48: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
48: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (7 ms)
48: [ RUN ] ClustsizeTest.MolDefaultCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 2, cmax: 4, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (10 ms)
48: [ RUN ] ClustsizeTest.MolShortCutoff
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 1, cmax: 6, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (9 ms)
48: [ RUN ] ClustsizeTest.MolCSize
48: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Total number of atoms in clusters = 8
48: cmid: 2, cmax: 4, max_size: 2
48: 50%100%cmid: 2, cmax: 6, max_size: 2
48: 50%100%[ OK ] ClustsizeTest.MolCSize (9 ms)
48: [----------] 5 tests from ClustsizeTest (44 ms total)
48:
48: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (2 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
48: Reading frames from gro file 'Test system', 8 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (10 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
48: Reading frames from gro file 'Test system', 8 atoms.
48:
Reading frame 0 time 0.000
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (10 ms)
48: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
48: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms)
48: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (25 ms total)
48:
48: [----------] 4 tests from ConvertTrjModuleTest
48: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (38 ms)
48: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (30 ms)
48: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (5 ms)
48: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
48: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
48:
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (5 ms)
48: [----------] 4 tests from ConvertTrjModuleTest (78 ms total)
48:
48: [----------] 3 tests from DistanceModuleTest
48: [ RUN ] DistanceModuleTest.ComputesDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2:
48: Number of samples: 5
48: Average distance: 1.43246 nm
48: Standard deviation: 0.96700 nm
48: [ OK ] DistanceModuleTest.ComputesDistances (10 ms)
48: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2:
48: Number of samples: 5
48: Average distance: 1.43246 nm
48: Standard deviation: 0.96700 nm
48: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
48: Number of samples: 4
48: Average distance: 1.81066 nm
48: Standard deviation: 0.79289 nm
48: [ OK ] DistanceModuleTest.ComputesMultipleDistances (12 ms)
48: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: atomname S1 S2 and res_cog x < 2.8:
48: Number of samples: 3
48: Average distance: 1.72076 nm
48: Standard deviation: 1.24839 nm
48: [ OK ] DistanceModuleTest.HandlesDynamicSelections (11 ms)
48: [----------] 3 tests from DistanceModuleTest (34 ms total)
48:
48: [----------] 2 tests from ExtractClusterModuleTest
48: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
48: trr version: GMX_trn_file (single precision)
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
48: Analyzed 26 frames, last time 0.050
48: There are 8 clusters containing 26 structures, highest framenr is 25
48: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (10 ms)
48: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
48: Analyzed 26 frames, last time 0.050
48: There are 8 clusters containing 26 structures, highest framenr is 25
48: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (8 ms)
48: [----------] 2 tests from ExtractClusterModuleTest (18 ms total)
48:
48: [----------] 2 tests from FreeVolumeModuleTest
48: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for CO2-RM. Set to zero.
48: Could not determine VDW radius for 40 particles. These were set to zero.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: cutoff = 0.18 nm
48: probe_radius = 0 nm
48: seed = 13
48: ninsert = 1000 probes per nm^3
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
48: van der Spoel and Luciano T. Costa
48: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
48: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
48: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
48: -------- -------- --- Thank You --- -------- --------
48:
48: Free volume 38.02 +/- 0.00 %
48: Total volume 68.92 +/- 0.00 nm^3
48: Number of molecules 340 total mass 63491.38 Dalton
48: Average molar mass: 186.74 Dalton
48: Density rho: 1529.71 +/- 0.00 nm^3
48: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
48: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
48: Fractional free volume 0.194 +/- 0.000
48: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (373 ms)
48: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: cutoff = 0.18 nm
48: probe_radius = 0 nm
48: seed = 17
48: ninsert = 1000 probes per nm^3
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
48: van der Spoel and Luciano T. Costa
48: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
48: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
48: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
48: -------- -------- --- Thank You --- -------- --------
48:
48: Free volume 38.48 +/- 0.00 %
48: Total volume 68.92 +/- 0.00 nm^3
48: Number of molecules 340 total mass 63491.38 Dalton
48: Average molar mass: 186.74 Dalton
48: Density rho: 1529.71 +/- 0.00 nm^3
48: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
48: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
48: Fractional free volume 0.200 +/- 0.000
48: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (354 ms)
48: [----------] 2 tests from FreeVolumeModuleTest (727 ms total)
48:
48: [----------] 9 tests from PairDistanceModuleTest
48: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesAllDistances (9 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (9 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (8 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (8 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (9 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (9 ms)
48: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (9 ms)
48: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (9 ms)
48: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (8 ms)
48: [----------] 9 tests from PairDistanceModuleTest (80 ms total)
48:
48: [----------] 5 tests from RdfModuleTest
48: [ RUN ] RdfModuleTest.BasicTest
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.BasicTest (72 ms)
48: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
48: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48: Analyzed 1 frames, last time 0.000
48: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (47 ms)
48: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (73 ms)
48: [ RUN ] RdfModuleTest.CalculatesSurf
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.CalculatesSurf (44 ms)
48: [ RUN ] RdfModuleTest.CalculatesXY
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] RdfModuleTest.CalculatesXY (84 ms)
48: [----------] 5 tests from RdfModuleTest (321 ms total)
48:
48: [----------] 5 tests from SasaModuleTest
48: [ RUN ] SasaModuleTest.BasicTest
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.BasicTest (46 ms)
48: [ RUN ] SasaModuleTest.HandlesSelectedResidues
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesSelectedResidues (31 ms)
48: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (24 ms)
48: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (26 ms)
48: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
48: Michael Scharf
48: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
48: of Surface Area and Volume and to Dot Surface Contouring of Molecular
48: Assemblies
48: J. Comp. Chem. 16 (1995) pp. 273-284
48: -------- -------- --- Thank You --- -------- --------
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
48: from the source below. This means the results may be different
48: compared to previous GROMACS versions.
48:
48: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
48: A. Bondi
48: van der Waals Volumes and Radii
48: J. Phys. Chem. 68 (1964) pp. 441-451
48: -------- -------- --- Thank You --- -------- --------
48:
48: Analyzed topology coordinates
48: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (26 ms)
48: [----------] 5 tests from SasaModuleTest (158 ms total)
48:
48: [----------] 8 tests from SelectModuleTest
48: [ RUN ] SelectModuleTest.BasicTest
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.BasicTest (15 ms)
48: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (12 ms)
48: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (12 ms)
48: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (12 ms)
48: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (12 ms)
48: [ RUN ] SelectModuleTest.NormalizesSizes
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.NormalizesSizes (8 ms)
48: [ RUN ] SelectModuleTest.WritesResidueNumbers
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.WritesResidueNumbers (8 ms)
48: [ RUN ] SelectModuleTest.WritesResidueIndices
48: Analyzed topology coordinates
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] SelectModuleTest.WritesResidueIndices (8 ms)
48: [----------] 8 tests from SelectModuleTest (90 ms total)
48:
48: [----------] 10 tests from SurfaceAreaTest
48: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
48: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
48: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
48: [ OK ] SurfaceAreaTest.ComputesTwoPoints (2 ms)
48: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
48: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (3 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints12
48: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints32
48: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints42
48: [ OK ] SurfaceAreaTest.SurfacePoints42 (1 ms)
48: [ RUN ] SurfaceAreaTest.SurfacePoints122
48: [ OK ] SurfaceAreaTest.SurfacePoints122 (2 ms)
48: [ RUN ] SurfaceAreaTest.Computes100Points
48: [ OK ] SurfaceAreaTest.Computes100Points (2 ms)
48: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
48: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (6 ms)
48: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
48: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (7 ms)
48: [----------] 10 tests from SurfaceAreaTest (27 ms total)
48:
48: [----------] 4 tests from TopologyInformation
48: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
48: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
48: [ RUN ] TopologyInformation.WorksWithGroFile
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TopologyInformation.WorksWithGroFile (11 ms)
48: [ RUN ] TopologyInformation.WorksWithPdbFile
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TopologyInformation.WorksWithPdbFile (11 ms)
48: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Generating 1-4 interactions: fudge = 0.5
48:
48: NOTE 2 [file lysozyme.top, line 1465]:
48: System has non-zero total charge: 2.000000
48: Total charge should normally be an integer. See
48: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
48: for discussion on how close it should be to an integer.
48:
48:
48:
48: Number of degrees of freedom in T-Coupling group rest is 465.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
48: Setting the LD random seed to -8519715
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48:
48: Generated 330891 of the 330891 1-4 parameter combinations
48:
48: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
48: Analysing residue names:
48: There are: 10 Protein residues
48: Analysing Protein...
48:
48: This run will generate roughly 0 Mb of data
48: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (2803 ms)
48: [----------] 4 tests from TopologyInformation (2826 ms total)
48:
48: [----------] 4 tests from TrajectoryModuleTest
48: [ RUN ] TrajectoryModuleTest.BasicTest
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.BasicTest (10 ms)
48: [ RUN ] TrajectoryModuleTest.PlotsXOnly
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.PlotsXOnly (10 ms)
48: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (9 ms)
48: [ RUN ] TrajectoryModuleTest.HandlesNoForces
48: Reading frames from gro file 'Test system', 15 atoms.
48:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
48: Analyzed 2 frames, last time 0.000
48:
48: WARNING: Masses and atomic (Van der Waals) radii will be guessed
48: based on residue and atom names, since they could not be
48: definitively assigned from the information in your input
48: files. These guessed numbers might deviate from the mass
48: and radius of the atom type. Please check the output
48: files if necessary.
48:
48: [ OK ] TrajectoryModuleTest.HandlesNoForces (10 ms)
48: [----------] 4 tests from TrajectoryModuleTest (40 ms total)
48:
48: [----------] 5 tests from UnionFinderTest
48: [ RUN ] UnionFinderTest.WorksEmpty
48: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
48: [ RUN ] UnionFinderTest.BasicMerges
48: [ OK ] UnionFinderTest.BasicMerges (0 ms)
48: [ RUN ] UnionFinderTest.LargerMerges
48: [ OK ] UnionFinderTest.LargerMerges (0 ms)
48: [ RUN ] UnionFinderTest.LongRightMerge
48: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
48: [ RUN ] UnionFinderTest.LongLeftMerge
48: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
48: [----------] 5 tests from UnionFinderTest (1 ms total)
48:
48: [----------] 1 test from MappedUnionFinderTest
48: [ RUN ] MappedUnionFinderTest.BasicMerges
48: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
48: [----------] 1 test from MappedUnionFinderTest (0 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 82 tests from 16 test cases ran. (4571 ms total)
48: [ PASSED ] 82 tests.
48/65 Test #48: TrajectoryAnalysisUnitTests ........... Passed 4.61 sec
test 49
Start 49: EnergyAnalysisUnitTests
49: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml"
49: Test timeout computed to be: 30
49: [==========] Running 7 tests from 4 test cases.
49: [----------] Global test environment set-up.
49: [----------] 1 test from DhdlTest
49: [ RUN ] DhdlTest.ExtractDhdl
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
49: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
49: Note: file tpx version 110, software tpx version 122
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
49:
49:
49: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
49: [ OK ] DhdlTest.ExtractDhdl (25 ms)
49: [----------] 1 test from DhdlTest (27 ms total)
49:
49: [----------] 1 test from OriresTest
49: [ RUN ] OriresTest.ExtractOrires
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
49: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
49: Note: file tpx version 111, software tpx version 122
49: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
49: End your selection with 0
49: Selecting all 7 orientation restraints
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
49: [ OK ] OriresTest.ExtractOrires (33 ms)
49: [----------] 1 test from OriresTest (33 ms total)
49:
49: [----------] 3 tests from EnergyTest
49: [ RUN ] EnergyTest.ExtractEnergy
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
49: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
49: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
49: [ OK ] EnergyTest.ExtractEnergy (11 ms)
49: [ RUN ] EnergyTest.ExtractEnergyByNumber
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
49: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
49: Pres. DC -268.49 3 8.52175 13.2804 (bar)
49: [ OK ] EnergyTest.ExtractEnergyByNumber (12 ms)
49: [ RUN ] EnergyTest.ExtractEnergyMixed
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
49: Select the terms you want from the following list by
49: selecting either (part of) the name or the number or a combination.
49: End your selection with an empty line or a zero.
49: -------------------------------------------------------------------
49: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
49: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
49: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
49: 13 Box-Z 14 Volume 15 Density 16 pV
49: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
49: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
49: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
49: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
49: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
49: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
49:
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: [ OK ] EnergyTest.ExtractEnergyMixed (11 ms)
49: [----------] 3 tests from EnergyTest (35 ms total)
49:
49: [----------] 2 tests from ViscosityTest
49: [ RUN ] ViscosityTest.EinsteinViscosity
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Pres-XX 20.2092 65 717.193 185.978 (bar)
49: Pres-XY -47.7351 39 372.522 207.456 (bar)
49: Pres-XZ 11.477 31 379.79 6.80818 (bar)
49: Pres-YX -47.7106 39 372.525 207.5 (bar)
49: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
49: Pres-YZ -41.3534 45 401.216 114.663 (bar)
49: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
49: Pres-ZY -41.3119 45 401.196 114.743 (bar)
49: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
49: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: [ OK ] ViscosityTest.EinsteinViscosity (21 ms)
49: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
49: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
49:
49: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
49: All statistics are over 5001 points
49:
49: Energy Average Err.Est. RMSD Tot-Drift
49: -------------------------------------------------------------------------------
49: Pres-XX 20.2092 65 717.193 185.978 (bar)
49: Pres-XY -47.7351 39 372.522 207.456 (bar)
49: Pres-XZ 11.477 31 379.79 6.80818 (bar)
49: Pres-YX -47.7106 39 372.525 207.5 (bar)
49: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
49: Pres-YZ -41.3534 45 401.216 114.663 (bar)
49: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
49: Pres-ZY -41.3119 45 401.196 114.743 (bar)
49: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
49: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
49: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
49: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
49: [ OK ] ViscosityTest.EinsteinViscosityIntegral (16 ms)
49: [----------] 2 tests from ViscosityTest (37 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 7 tests from 4 test cases ran. (133 ms total)
49: [ PASSED ] 7 tests.
49/65 Test #49: EnergyAnalysisUnitTests ............... Passed 0.17 sec
test 50
Start 50: ToolUnitTests
50: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ToolUnitTests.xml"
50: Test timeout computed to be: 1920
50: [==========] Running 21 tests from 5 test cases.
50: [----------] Global test environment set-up.
50: [----------] 2 tests from DumpTest
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: For a correct single-point energy evaluation with nsteps = 0, use
50: continuation = yes to avoid constraining the input coordinates.
50:
50: Generating 1-4 interactions: fudge = 0.5
50:
50: NOTE 2 [file lysozyme.top, line 1465]:
50: System has non-zero total charge: 2.000000
50: Total charge should normally be an integer. See
50: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
50: for discussion on how close it should be to an integer.
50:
50:
50:
50: Number of degrees of freedom in T-Coupling group rest is 465.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: NVE simulation with an initial temperature of zero: will use a Verlet
50: buffer of 10%. Check your energy drift!
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Setting the LD random seed to -1074335746
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50:
50: Generated 330891 of the 330891 1-4 parameter combinations
50:
50: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
50: Analysing residue names:
50: There are: 10 Protein residues
50: Analysing Protein...
50:
50: This run will generate roughly 0 Mb of data
50: [ RUN ] DumpTest.WorksWithTpr
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
50: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
50: inputrec:
50: integrator = md
50: tinit = 0
50: dt = 0.001
50: nsteps = 0
50: init-step = 0
50: simulation-part = 1
50: mts = false
50: comm-mode = Linear
50: nstcomm = 100
50: bd-fric = 0
50: ld-seed = -1074335746
50: emtol = 10
50: emstep = 0.01
50: niter = 20
50: fcstep = 0
50: nstcgsteep = 1000
50: nbfgscorr = 10
50: rtpi = 0.05
50: nstxout = 0
50: nstvout = 0
50: nstfout = 0
50: nstlog = 1000
50: nstcalcenergy = 100
50: nstenergy = 1000
50: nstxout-compressed = 0
50: compressed-x-precision = 1000
50: cutoff-scheme = Verlet
50: nstlist = 10
50: pbc = xyz
50: periodic-molecules = false
50: verlet-buffer-tolerance = -1
50: rlist = 1.1
50: coulombtype = Cut-off
50: coulomb-modifier = Potential-shift
50: rcoulomb-switch = 0
50: rcoulomb = 1
50: epsilon-r = 1
50: epsilon-rf = inf
50: vdw-type = Cut-off
50: vdw-modifier = Potential-shift
50: rvdw-switch = 0
50: rvdw = 1
50: DispCorr = No
50: table-extension = 1
50: fourierspacing = 0.12
50: fourier-nx = 0
50: fourier-ny = 0
50: fourier-nz = 0
50: pme-order = 4
50: ewald-rtol = 1e-05
50: ewald-rtol-lj = 0.001
50: lj-pme-comb-rule = Geometric
50: ewald-geometry = 0
50: epsilon-surface = 0
50: tcoupl = No
50: nsttcouple = -1
50: nh-chain-length = 0
50: print-nose-hoover-chain-variables = false
50: pcoupl = No
50: pcoupltype = Isotropic
50: nstpcouple = -1
50: tau-p = 1
50: compressibility (3x3):
50: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p (3x3):
50: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: refcoord-scaling = No
50: posres-com (3):
50: posres-com[0]= 0.00000e+00
50: posres-com[1]= 0.00000e+00
50: posres-com[2]= 0.00000e+00
50: posres-comB (3):
50: posres-comB[0]= 0.00000e+00
50: posres-comB[1]= 0.00000e+00
50: posres-comB[2]= 0.00000e+00
50: QMMM = false
50: qm-opts:
50: ngQM = 0
50: constraint-algorithm = Lincs
50: continuation = false
50: Shake-SOR = false
50: shake-tol = 0.0001
50: lincs-order = 4
50: lincs-iter = 1
50: lincs-warnangle = 30
50: nwall = 0
50: wall-type = 9-3
50: wall-r-linpot = -1
50: wall-atomtype[0] = -1
50: wall-atomtype[1] = -1
50: wall-density[0] = 0
50: wall-density[1] = 0
50: wall-ewald-zfac = 3
50: pull = false
50: awh = false
50: rotation = false
50: interactiveMD = false
50: disre = No
50: disre-weighting = Conservative
50: disre-mixed = false
50: dr-fc = 1000
50: dr-tau = 0
50: nstdisreout = 100
50: orire-fc = 0
50: orire-tau = 0
50: nstorireout = 100
50: free-energy = no
50: cos-acceleration = 0
50: deform (3x3):
50: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: simulated-tempering = false
50: swapcoords = no
50: userint1 = 0
50: userint2 = 0
50: userint3 = 0
50: userint4 = 0
50: userreal1 = 0
50: userreal2 = 0
50: userreal3 = 0
50: userreal4 = 0
50: applied-forces:
50: electric-field:
50: x:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: y:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: z:
50: E0 = 0
50: omega = 0
50: t0 = 0
50: sigma = 0
50: density-guided-simulation:
50: active = false
50: group = protein
50: similarity-measure = inner-product
50: atom-spreading-weight = unity
50: force-constant = 1e+09
50: gaussian-transform-spreading-width = 0.2
50: gaussian-transform-spreading-range-in-multiples-of-width = 4
50: reference-density-filename = reference.mrc
50: nst = 1
50: normalize-densities = true
50: adaptive-force-scaling = false
50: adaptive-force-scaling-time-constant = 4
50: shift-vector =
50: transformation-matrix =
50: grpopts:
50: nrdf: 465
50: ref-t: 0
50: tau-t: 0
50: annealing: No
50: annealing-npoints: 0
50: acc: 0 0 0
50: nfreeze: N N N
50: energygrp-flags[ 0]: 0
50: header:
50: bIr = present
50: bBox = present
50: bTop = present
50: bX = present
50: bV = present
50: bF = not present
50: natoms = 156
50: lambda = 0.000000e+00
50: buffer size = 70158
50: topology:
50: name="First 10 residues from 1AKI"
50: #atoms = 156
50: #molblock = 1
50: molblock (0):
50: moltype = 0 "Protein_chain_B"
50: #molecules = 1
50: #posres_xA = 0
50: #posres_xB = 0
50: bIntermolecularInteractions = false
50: ffparams:
50: atnr=10
50: ntypes=212
50: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06
50: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
50: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
50: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
50: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
50: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
50: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
50: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
50: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
50: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
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50: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
50: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06
50: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
50: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
50: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
50: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
50: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
50: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
50: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
50: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
50: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
50: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08
50: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
50: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
50: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
50: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
50: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
50: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
50: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
50: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
50: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
50: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05
50: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
50: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
50: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
50: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
50: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
50: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
50: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
50: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
50: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
50: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06
50: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
50: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
50: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
50: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
50: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
50: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
50: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
50: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
50: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
50: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06
50: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
50: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
50: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
50: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
50: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
50: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
50: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
50: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
50: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
50: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08
50: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
50: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
50: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
50: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
50: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
50: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
50: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
50: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
50: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
50: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08
50: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
50: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
50: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
50: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
50: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
50: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
50: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
50: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
50: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
50: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
50: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05
50: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
50: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
50: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
50: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
50: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
50: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
50: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
50: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
50: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
50: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
50: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
50: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
50: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
50: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
50: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
50: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
50: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
50: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
50: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
50: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
50: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
50: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
50: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
50: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
50: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
50: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
50: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
50: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
50: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
50: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
50: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
50: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
50: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
50: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
50: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
50: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
50: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
50: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
50: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
50: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
50: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2
50: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2
50: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2
50: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
50: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
50: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07
50: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06
50: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06
50: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06
50: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
50: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07
50: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06
50: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08
50: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07
50: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06
50: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07
50: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06
50: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06
50: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06
50: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06
50: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07
50: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07
50: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07
50: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06
50: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06
50: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08
50: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07
50: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08
50: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06
50: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07
50: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05
50: reppow = 12
50: fudgeQQ = 0.5
50: cmap
50: atomtypes:
50: atomtype[ 0]={atomnumber= 7}
50: atomtype[ 1]={atomnumber= 1}
50: atomtype[ 2]={atomnumber= 6}
50: atomtype[ 3]={atomnumber= 1}
50: atomtype[ 4]={atomnumber= 6}
50: atomtype[ 5]={atomnumber= 8}
50: atomtype[ 6]={atomnumber= 6}
50: atomtype[ 7]={atomnumber= 1}
50: atomtype[ 8]={atomnumber= 6}
50: atomtype[ 9]={atomnumber= 16}
50: moltype (0):
50: name="Protein_chain_B"
50: atoms:
50: atom (156):
50: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
50: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
50: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
50: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
50: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
50: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
50: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
50: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
50: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
50: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
50: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
50: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
50: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
50: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
50: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
50: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
50: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
50: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
50: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
50: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
50: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
50: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
50: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
50: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
50: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
50: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
50: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
50: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
50: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
50: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
50: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
50: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
50: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
50: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
50: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
50: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
50: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
50: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
50: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
50: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
50: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
50: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
50: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
50: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
50: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
50: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
50: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
50: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
50: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
50: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
50: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
50: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
50: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
50: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
50: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
50: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
50: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
50: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
50: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
50: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
50: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
50: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
50: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
50: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
50: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
50: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
50: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
50: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
50: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
50: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
50: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
50: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
50: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
50: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
50: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
50: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
50: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
50: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
50: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
50: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
50: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
50: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
50: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
50: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
50: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
50: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
50: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
50: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
50: atom (156):
50: atom[0]={name="N"}
50: atom[1]={name="H1"}
50: atom[2]={name="H2"}
50: atom[3]={name="H3"}
50: atom[4]={name="CA"}
50: atom[5]={name="HA"}
50: atom[6]={name="CB"}
50: atom[7]={name="HB1"}
50: atom[8]={name="HB2"}
50: atom[9]={name="CG"}
50: atom[10]={name="HG1"}
50: atom[11]={name="HG2"}
50: atom[12]={name="CD"}
50: atom[13]={name="HD1"}
50: atom[14]={name="HD2"}
50: atom[15]={name="CE"}
50: atom[16]={name="HE1"}
50: atom[17]={name="HE2"}
50: atom[18]={name="NZ"}
50: atom[19]={name="HZ1"}
50: atom[20]={name="HZ2"}
50: atom[21]={name="HZ3"}
50: atom[22]={name="C"}
50: atom[23]={name="O"}
50: atom[24]={name="N"}
50: atom[25]={name="H"}
50: atom[26]={name="CA"}
50: atom[27]={name="HA"}
50: atom[28]={name="CB"}
50: atom[29]={name="HB"}
50: atom[30]={name="CG1"}
50: atom[31]={name="HG11"}
50: atom[32]={name="HG12"}
50: atom[33]={name="HG13"}
50: atom[34]={name="CG2"}
50: atom[35]={name="HG21"}
50: atom[36]={name="HG22"}
50: atom[37]={name="HG23"}
50: atom[38]={name="C"}
50: atom[39]={name="O"}
50: atom[40]={name="N"}
50: atom[41]={name="H"}
50: atom[42]={name="CA"}
50: atom[43]={name="HA"}
50: atom[44]={name="CB"}
50: atom[45]={name="HB1"}
50: atom[46]={name="HB2"}
50: atom[47]={name="CG"}
50: atom[48]={name="CD1"}
50: atom[49]={name="HD1"}
50: atom[50]={name="CD2"}
50: atom[51]={name="HD2"}
50: atom[52]={name="CE1"}
50: atom[53]={name="HE1"}
50: atom[54]={name="CE2"}
50: atom[55]={name="HE2"}
50: atom[56]={name="CZ"}
50: atom[57]={name="HZ"}
50: atom[58]={name="C"}
50: atom[59]={name="O"}
50: atom[60]={name="N"}
50: atom[61]={name="H"}
50: atom[62]={name="CA"}
50: atom[63]={name="HA1"}
50: atom[64]={name="HA2"}
50: atom[65]={name="C"}
50: atom[66]={name="O"}
50: atom[67]={name="N"}
50: atom[68]={name="H"}
50: atom[69]={name="CA"}
50: atom[70]={name="HA"}
50: atom[71]={name="CB"}
50: atom[72]={name="HB1"}
50: atom[73]={name="HB2"}
50: atom[74]={name="CG"}
50: atom[75]={name="HG1"}
50: atom[76]={name="HG2"}
50: atom[77]={name="CD"}
50: atom[78]={name="HD1"}
50: atom[79]={name="HD2"}
50: atom[80]={name="NE"}
50: atom[81]={name="HE"}
50: atom[82]={name="CZ"}
50: atom[83]={name="NH1"}
50: atom[84]={name="HH11"}
50: atom[85]={name="HH12"}
50: atom[86]={name="NH2"}
50: atom[87]={name="HH21"}
50: atom[88]={name="HH22"}
50: atom[89]={name="C"}
50: atom[90]={name="O"}
50: atom[91]={name="N"}
50: atom[92]={name="H"}
50: atom[93]={name="CA"}
50: atom[94]={name="HA"}
50: atom[95]={name="CB"}
50: atom[96]={name="HB1"}
50: atom[97]={name="HB2"}
50: atom[98]={name="SG"}
50: atom[99]={name="HG"}
50: atom[100]={name="C"}
50: atom[101]={name="O"}
50: atom[102]={name="N"}
50: atom[103]={name="H"}
50: atom[104]={name="CA"}
50: atom[105]={name="HA"}
50: atom[106]={name="CB"}
50: atom[107]={name="HB1"}
50: atom[108]={name="HB2"}
50: atom[109]={name="CG"}
50: atom[110]={name="HG1"}
50: atom[111]={name="HG2"}
50: atom[112]={name="CD"}
50: atom[113]={name="OE1"}
50: atom[114]={name="OE2"}
50: atom[115]={name="C"}
50: atom[116]={name="O"}
50: atom[117]={name="N"}
50: atom[118]={name="H"}
50: atom[119]={name="CA"}
50: atom[120]={name="HA"}
50: atom[121]={name="CB"}
50: atom[122]={name="HB1"}
50: atom[123]={name="HB2"}
50: atom[124]={name="CG"}
50: atom[125]={name="HG"}
50: atom[126]={name="CD1"}
50: atom[127]={name="HD11"}
50: atom[128]={name="HD12"}
50: atom[129]={name="HD13"}
50: atom[130]={name="CD2"}
50: atom[131]={name="HD21"}
50: atom[132]={name="HD22"}
50: atom[133]={name="HD23"}
50: atom[134]={name="C"}
50: atom[135]={name="O"}
50: atom[136]={name="N"}
50: atom[137]={name="H"}
50: atom[138]={name="CA"}
50: atom[139]={name="HA"}
50: atom[140]={name="CB"}
50: atom[141]={name="HB1"}
50: atom[142]={name="HB2"}
50: atom[143]={name="HB3"}
50: atom[144]={name="C"}
50: atom[145]={name="O"}
50: atom[146]={name="N"}
50: atom[147]={name="H"}
50: atom[148]={name="CA"}
50: atom[149]={name="HA"}
50: atom[150]={name="CB"}
50: atom[151]={name="HB1"}
50: atom[152]={name="HB2"}
50: atom[153]={name="HB3"}
50: atom[154]={name="C"}
50: atom[155]={name="O"}
50: type (156):
50: type[0]={name="opls_287",nameB="opls_287"}
50: type[1]={name="opls_290",nameB="opls_290"}
50: type[2]={name="opls_290",nameB="opls_290"}
50: type[3]={name="opls_290",nameB="opls_290"}
50: type[4]={name="opls_293B",nameB="opls_293B"}
50: type[5]={name="opls_140",nameB="opls_140"}
50: type[6]={name="opls_136",nameB="opls_136"}
50: type[7]={name="opls_140",nameB="opls_140"}
50: type[8]={name="opls_140",nameB="opls_140"}
50: type[9]={name="opls_136",nameB="opls_136"}
50: type[10]={name="opls_140",nameB="opls_140"}
50: type[11]={name="opls_140",nameB="opls_140"}
50: type[12]={name="opls_136",nameB="opls_136"}
50: type[13]={name="opls_140",nameB="opls_140"}
50: type[14]={name="opls_140",nameB="opls_140"}
50: type[15]={name="opls_292",nameB="opls_292"}
50: type[16]={name="opls_140",nameB="opls_140"}
50: type[17]={name="opls_140",nameB="opls_140"}
50: type[18]={name="opls_287",nameB="opls_287"}
50: type[19]={name="opls_290",nameB="opls_290"}
50: type[20]={name="opls_290",nameB="opls_290"}
50: type[21]={name="opls_290",nameB="opls_290"}
50: type[22]={name="opls_235",nameB="opls_235"}
50: type[23]={name="opls_236",nameB="opls_236"}
50: type[24]={name="opls_238",nameB="opls_238"}
50: type[25]={name="opls_241",nameB="opls_241"}
50: type[26]={name="opls_224B",nameB="opls_224B"}
50: type[27]={name="opls_140",nameB="opls_140"}
50: type[28]={name="opls_137",nameB="opls_137"}
50: type[29]={name="opls_140",nameB="opls_140"}
50: type[30]={name="opls_135",nameB="opls_135"}
50: type[31]={name="opls_140",nameB="opls_140"}
50: type[32]={name="opls_140",nameB="opls_140"}
50: type[33]={name="opls_140",nameB="opls_140"}
50: type[34]={name="opls_135",nameB="opls_135"}
50: type[35]={name="opls_140",nameB="opls_140"}
50: type[36]={name="opls_140",nameB="opls_140"}
50: type[37]={name="opls_140",nameB="opls_140"}
50: type[38]={name="opls_235",nameB="opls_235"}
50: type[39]={name="opls_236",nameB="opls_236"}
50: type[40]={name="opls_238",nameB="opls_238"}
50: type[41]={name="opls_241",nameB="opls_241"}
50: type[42]={name="opls_224B",nameB="opls_224B"}
50: type[43]={name="opls_140",nameB="opls_140"}
50: type[44]={name="opls_149",nameB="opls_149"}
50: type[45]={name="opls_140",nameB="opls_140"}
50: type[46]={name="opls_140",nameB="opls_140"}
50: type[47]={name="opls_145",nameB="opls_145"}
50: type[48]={name="opls_145",nameB="opls_145"}
50: type[49]={name="opls_146",nameB="opls_146"}
50: type[50]={name="opls_145",nameB="opls_145"}
50: type[51]={name="opls_146",nameB="opls_146"}
50: type[52]={name="opls_145",nameB="opls_145"}
50: type[53]={name="opls_146",nameB="opls_146"}
50: type[54]={name="opls_145",nameB="opls_145"}
50: type[55]={name="opls_146",nameB="opls_146"}
50: type[56]={name="opls_145",nameB="opls_145"}
50: type[57]={name="opls_146",nameB="opls_146"}
50: type[58]={name="opls_235",nameB="opls_235"}
50: type[59]={name="opls_236",nameB="opls_236"}
50: type[60]={name="opls_238",nameB="opls_238"}
50: type[61]={name="opls_241",nameB="opls_241"}
50: type[62]={name="opls_223B",nameB="opls_223B"}
50: type[63]={name="opls_140",nameB="opls_140"}
50: type[64]={name="opls_140",nameB="opls_140"}
50: type[65]={name="opls_235",nameB="opls_235"}
50: type[66]={name="opls_236",nameB="opls_236"}
50: type[67]={name="opls_238",nameB="opls_238"}
50: type[68]={name="opls_241",nameB="opls_241"}
50: type[69]={name="opls_224B",nameB="opls_224B"}
50: type[70]={name="opls_140",nameB="opls_140"}
50: type[71]={name="opls_136",nameB="opls_136"}
50: type[72]={name="opls_140",nameB="opls_140"}
50: type[73]={name="opls_140",nameB="opls_140"}
50: type[74]={name="opls_308",nameB="opls_308"}
50: type[75]={name="opls_140",nameB="opls_140"}
50: type[76]={name="opls_140",nameB="opls_140"}
50: type[77]={name="opls_307",nameB="opls_307"}
50: type[78]={name="opls_140",nameB="opls_140"}
50: type[79]={name="opls_140",nameB="opls_140"}
50: type[80]={name="opls_303",nameB="opls_303"}
50: type[81]={name="opls_304",nameB="opls_304"}
50: type[82]={name="opls_302",nameB="opls_302"}
50: type[83]={name="opls_300",nameB="opls_300"}
50: type[84]={name="opls_301",nameB="opls_301"}
50: type[85]={name="opls_301",nameB="opls_301"}
50: type[86]={name="opls_300",nameB="opls_300"}
50: type[87]={name="opls_301",nameB="opls_301"}
50: type[88]={name="opls_301",nameB="opls_301"}
50: type[89]={name="opls_235",nameB="opls_235"}
50: type[90]={name="opls_236",nameB="opls_236"}
50: type[91]={name="opls_238",nameB="opls_238"}
50: type[92]={name="opls_241",nameB="opls_241"}
50: type[93]={name="opls_224B",nameB="opls_224B"}
50: type[94]={name="opls_140",nameB="opls_140"}
50: type[95]={name="opls_206",nameB="opls_206"}
50: type[96]={name="opls_140",nameB="opls_140"}
50: type[97]={name="opls_140",nameB="opls_140"}
50: type[98]={name="opls_200",nameB="opls_200"}
50: type[99]={name="opls_204",nameB="opls_204"}
50: type[100]={name="opls_235",nameB="opls_235"}
50: type[101]={name="opls_236",nameB="opls_236"}
50: type[102]={name="opls_238",nameB="opls_238"}
50: type[103]={name="opls_241",nameB="opls_241"}
50: type[104]={name="opls_224B",nameB="opls_224B"}
50: type[105]={name="opls_140",nameB="opls_140"}
50: type[106]={name="opls_136",nameB="opls_136"}
50: type[107]={name="opls_140",nameB="opls_140"}
50: type[108]={name="opls_140",nameB="opls_140"}
50: type[109]={name="opls_274",nameB="opls_274"}
50: type[110]={name="opls_140",nameB="opls_140"}
50: type[111]={name="opls_140",nameB="opls_140"}
50: type[112]={name="opls_271",nameB="opls_271"}
50: type[113]={name="opls_272",nameB="opls_272"}
50: type[114]={name="opls_272",nameB="opls_272"}
50: type[115]={name="opls_235",nameB="opls_235"}
50: type[116]={name="opls_236",nameB="opls_236"}
50: type[117]={name="opls_238",nameB="opls_238"}
50: type[118]={name="opls_241",nameB="opls_241"}
50: type[119]={name="opls_224B",nameB="opls_224B"}
50: type[120]={name="opls_140",nameB="opls_140"}
50: type[121]={name="opls_136",nameB="opls_136"}
50: type[122]={name="opls_140",nameB="opls_140"}
50: type[123]={name="opls_140",nameB="opls_140"}
50: type[124]={name="opls_137",nameB="opls_137"}
50: type[125]={name="opls_140",nameB="opls_140"}
50: type[126]={name="opls_135",nameB="opls_135"}
50: type[127]={name="opls_140",nameB="opls_140"}
50: type[128]={name="opls_140",nameB="opls_140"}
50: type[129]={name="opls_140",nameB="opls_140"}
50: type[130]={name="opls_135",nameB="opls_135"}
50: type[131]={name="opls_140",nameB="opls_140"}
50: type[132]={name="opls_140",nameB="opls_140"}
50: type[133]={name="opls_140",nameB="opls_140"}
50: type[134]={name="opls_235",nameB="opls_235"}
50: type[135]={name="opls_236",nameB="opls_236"}
50: type[136]={name="opls_238",nameB="opls_238"}
50: type[137]={name="opls_241",nameB="opls_241"}
50: type[138]={name="opls_224B",nameB="opls_224B"}
50: type[139]={name="opls_140",nameB="opls_140"}
50: type[140]={name="opls_135",nameB="opls_135"}
50: type[141]={name="opls_140",nameB="opls_140"}
50: type[142]={name="opls_140",nameB="opls_140"}
50: type[143]={name="opls_140",nameB="opls_140"}
50: type[144]={name="opls_235",nameB="opls_235"}
50: type[145]={name="opls_236",nameB="opls_236"}
50: type[146]={name="opls_238",nameB="opls_238"}
50: type[147]={name="opls_241",nameB="opls_241"}
50: type[148]={name="opls_224B",nameB="opls_224B"}
50: type[149]={name="opls_140",nameB="opls_140"}
50: type[150]={name="opls_135",nameB="opls_135"}
50: type[151]={name="opls_140",nameB="opls_140"}
50: type[152]={name="opls_140",nameB="opls_140"}
50: type[153]={name="opls_140",nameB="opls_140"}
50: type[154]={name="opls_235",nameB="opls_235"}
50: type[155]={name="opls_236",nameB="opls_236"}
50: residue (10):
50: residue[0]={name="LYS", nr=1, ic=' '}
50: residue[1]={name="VAL", nr=2, ic=' '}
50: residue[2]={name="PHE", nr=3, ic=' '}
50: residue[3]={name="GLY", nr=4, ic=' '}
50: residue[4]={name="ARG", nr=5, ic=' '}
50: residue[5]={name="CYS", nr=6, ic=' '}
50: residue[6]={name="GLU", nr=7, ic=' '}
50: residue[7]={name="LEU", nr=8, ic=' '}
50: residue[8]={name="ALA", nr=9, ic=' '}
50: residue[9]={name="ALA", nr=10, ic=' '}
50: excls:
50: numLists=156
50: numElements=1828
50: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
50: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22}
50: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
50: 23, 24, 25, 26}
50: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
50: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
50: 14, 15, 22, 23, 24}
50: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
50: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
50: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
50: 16, 17, 18, 22}
50: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
50: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
50: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
50: 17, 18, 19, 20, 21}
50: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
50: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
50: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
50: 20, 21}
50: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
50: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21}
50: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25,
50: 26, 27, 28, 38}
50: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26}
50: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
50: 30, 34, 38, 39, 40}
50: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38}
50: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
50: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
50: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
50: 40}
50: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
50: 34, 35, 36, 37, 38, 39, 40}
50: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34}
50: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
50: 36, 37, 38}
50: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37}
50: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
50: 40, 41, 42, 43, 44, 58}
50: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42}
50: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
50: 45, 46, 47, 58, 59, 60}
50: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58}
50: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
50: 48, 50, 58, 59, 60, 61, 62}
50: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
50: 60}
50: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
50: 50, 51, 52, 54, 58, 59, 60}
50: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
50: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
50: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
50: 52, 53, 54, 55, 56, 58}
50: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
50: 54, 56, 57}
50: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56}
50: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
50: 55, 56, 57}
50: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56}
50: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
50: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57}
50: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
50: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57}
50: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
50: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57}
50: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
50: 60, 61, 62, 63, 64, 65}
50: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62}
50: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
50: 65, 66, 67}
50: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65}
50: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
50: 68, 69}
50: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67}
50: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67}
50: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
50: 70, 71, 89}
50: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69}
50: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
50: 72, 73, 74, 89, 90, 91}
50: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89}
50: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
50: 75, 76, 77, 89, 90, 91, 92, 93}
50: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
50: 91}
50: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
50: 77, 78, 79, 80, 89, 90, 91}
50: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
50: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
50: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
50: 79, 80, 81, 82, 89}
50: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
50: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
50: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
50: 81, 82, 83, 86}
50: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
50: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
50: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
50: 84, 85, 86, 87, 88}
50: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86}
50: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,
50: 87, 88}
50: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
50: excls[84][num=6]={80, 82, 83, 84, 85, 86}
50: excls[85][num=6]={80, 82, 83, 84, 85, 86}
50: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
50: excls[87][num=6]={80, 82, 83, 86, 87, 88}
50: excls[88][num=6]={80, 82, 83, 86, 87, 88}
50: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
50: 91, 92, 93, 94, 95, 100}
50: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93}
50: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95,
50: 96, 97, 98, 100, 101, 102}
50: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100}
50: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98,
50: 99, 100, 101, 102, 103, 104}
50: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101,
50: 102}
50: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100,
50: 101, 102}
50: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100}
50: excls[99][num=6]={93, 95, 96, 97, 98, 99}
50: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101,
50: 102, 103, 104, 105, 106, 115}
50: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104}
50: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105,
50: 106, 107, 108, 109, 115, 116, 117}
50: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115}
50: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107,
50: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
50: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 115, 116, 117}
50: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 110, 111, 112, 113, 114, 115, 116, 117}
50: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 115}
50: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 115}
50: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111,
50: 112, 113, 114, 115}
50: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113,
50: 114}
50: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114}
50: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114}
50: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109,
50: 115, 116, 117, 118, 119, 120, 121, 134}
50: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119}
50: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119,
50: 120, 121, 122, 123, 124, 134, 135, 136}
50: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134}
50: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122,
50: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
50: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 134, 135, 136}
50: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136}
50: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 130, 134}
50: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 130, 134}
50: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126,
50: 127, 128, 129, 130, 131, 132, 133, 134}
50: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130}
50: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128,
50: 129, 130, 131, 132, 133}
50: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133}
50: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124,
50: 134, 135, 136, 137, 138, 139, 140, 144}
50: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138}
50: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138,
50: 139, 140, 141, 142, 143, 144, 145, 146}
50: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144}
50: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141,
50: 142, 143, 144, 145, 146, 147, 148}
50: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146}
50: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146}
50: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144}
50: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143,
50: 144, 145, 146, 147, 148, 149, 150, 154}
50: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148}
50: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148,
50: 149, 150, 151, 152, 153, 154, 155}
50: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154}
50: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151,
50: 152, 153, 154, 155}
50: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154}
50: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153,
50: 154, 155}
50: excls[155][num=6]={146, 148, 149, 150, 154, 155}
50: Bond:
50: nr: 468
50: iatoms:
50: 0 type=100 (BONDS) 0 1
50: 1 type=100 (BONDS) 0 2
50: 2 type=100 (BONDS) 0 3
50: 3 type=101 (BONDS) 0 4
50: 4 type=102 (BONDS) 4 5
50: 5 type=103 (BONDS) 4 6
50: 6 type=104 (BONDS) 4 22
50: 7 type=102 (BONDS) 6 7
50: 8 type=102 (BONDS) 6 8
50: 9 type=103 (BONDS) 6 9
50: 10 type=102 (BONDS) 9 10
50: 11 type=102 (BONDS) 9 11
50: 12 type=103 (BONDS) 9 12
50: 13 type=102 (BONDS) 12 13
50: 14 type=102 (BONDS) 12 14
50: 15 type=103 (BONDS) 12 15
50: 16 type=102 (BONDS) 15 16
50: 17 type=102 (BONDS) 15 17
50: 18 type=101 (BONDS) 15 18
50: 19 type=100 (BONDS) 18 19
50: 20 type=100 (BONDS) 18 20
50: 21 type=100 (BONDS) 18 21
50: 22 type=105 (BONDS) 22 23
50: 23 type=106 (BONDS) 22 24
50: 24 type=100 (BONDS) 24 25
50: 25 type=107 (BONDS) 24 26
50: 26 type=102 (BONDS) 26 27
50: 27 type=103 (BONDS) 26 28
50: 28 type=104 (BONDS) 26 38
50: 29 type=102 (BONDS) 28 29
50: 30 type=103 (BONDS) 28 30
50: 31 type=103 (BONDS) 28 34
50: 32 type=102 (BONDS) 30 31
50: 33 type=102 (BONDS) 30 32
50: 34 type=102 (BONDS) 30 33
50: 35 type=102 (BONDS) 34 35
50: 36 type=102 (BONDS) 34 36
50: 37 type=102 (BONDS) 34 37
50: 38 type=105 (BONDS) 38 39
50: 39 type=106 (BONDS) 38 40
50: 40 type=100 (BONDS) 40 41
50: 41 type=107 (BONDS) 40 42
50: 42 type=102 (BONDS) 42 43
50: 43 type=103 (BONDS) 42 44
50: 44 type=104 (BONDS) 42 58
50: 45 type=102 (BONDS) 44 45
50: 46 type=102 (BONDS) 44 46
50: 47 type=108 (BONDS) 44 47
50: 48 type=109 (BONDS) 47 48
50: 49 type=109 (BONDS) 47 50
50: 50 type=110 (BONDS) 48 49
50: 51 type=109 (BONDS) 48 52
50: 52 type=110 (BONDS) 50 51
50: 53 type=109 (BONDS) 50 54
50: 54 type=110 (BONDS) 52 53
50: 55 type=109 (BONDS) 52 56
50: 56 type=110 (BONDS) 54 55
50: 57 type=109 (BONDS) 54 56
50: 58 type=110 (BONDS) 56 57
50: 59 type=105 (BONDS) 58 59
50: 60 type=106 (BONDS) 58 60
50: 61 type=100 (BONDS) 60 61
50: 62 type=107 (BONDS) 60 62
50: 63 type=102 (BONDS) 62 63
50: 64 type=102 (BONDS) 62 64
50: 65 type=104 (BONDS) 62 65
50: 66 type=105 (BONDS) 65 66
50: 67 type=106 (BONDS) 65 67
50: 68 type=100 (BONDS) 67 68
50: 69 type=107 (BONDS) 67 69
50: 70 type=102 (BONDS) 69 70
50: 71 type=103 (BONDS) 69 71
50: 72 type=104 (BONDS) 69 89
50: 73 type=102 (BONDS) 71 72
50: 74 type=102 (BONDS) 71 73
50: 75 type=103 (BONDS) 71 74
50: 76 type=102 (BONDS) 74 75
50: 77 type=102 (BONDS) 74 76
50: 78 type=103 (BONDS) 74 77
50: 79 type=102 (BONDS) 77 78
50: 80 type=102 (BONDS) 77 79
50: 81 type=111 (BONDS) 77 80
50: 82 type=100 (BONDS) 80 81
50: 83 type=112 (BONDS) 80 82
50: 84 type=112 (BONDS) 82 83
50: 85 type=112 (BONDS) 82 86
50: 86 type=100 (BONDS) 83 84
50: 87 type=100 (BONDS) 83 85
50: 88 type=100 (BONDS) 86 87
50: 89 type=100 (BONDS) 86 88
50: 90 type=105 (BONDS) 89 90
50: 91 type=106 (BONDS) 89 91
50: 92 type=100 (BONDS) 91 92
50: 93 type=107 (BONDS) 91 93
50: 94 type=102 (BONDS) 93 94
50: 95 type=103 (BONDS) 93 95
50: 96 type=104 (BONDS) 93 100
50: 97 type=102 (BONDS) 95 96
50: 98 type=102 (BONDS) 95 97
50: 99 type=113 (BONDS) 95 98
50: 100 type=114 (BONDS) 98 99
50: 101 type=105 (BONDS) 100 101
50: 102 type=106 (BONDS) 100 102
50: 103 type=100 (BONDS) 102 103
50: 104 type=107 (BONDS) 102 104
50: 105 type=102 (BONDS) 104 105
50: 106 type=103 (BONDS) 104 106
50: 107 type=104 (BONDS) 104 115
50: 108 type=102 (BONDS) 106 107
50: 109 type=102 (BONDS) 106 108
50: 110 type=103 (BONDS) 106 109
50: 111 type=102 (BONDS) 109 110
50: 112 type=102 (BONDS) 109 111
50: 113 type=104 (BONDS) 109 112
50: 114 type=115 (BONDS) 112 113
50: 115 type=115 (BONDS) 112 114
50: 116 type=105 (BONDS) 115 116
50: 117 type=106 (BONDS) 115 117
50: 118 type=100 (BONDS) 117 118
50: 119 type=107 (BONDS) 117 119
50: 120 type=102 (BONDS) 119 120
50: 121 type=103 (BONDS) 119 121
50: 122 type=104 (BONDS) 119 134
50: 123 type=102 (BONDS) 121 122
50: 124 type=102 (BONDS) 121 123
50: 125 type=103 (BONDS) 121 124
50: 126 type=102 (BONDS) 124 125
50: 127 type=103 (BONDS) 124 126
50: 128 type=103 (BONDS) 124 130
50: 129 type=102 (BONDS) 126 127
50: 130 type=102 (BONDS) 126 128
50: 131 type=102 (BONDS) 126 129
50: 132 type=102 (BONDS) 130 131
50: 133 type=102 (BONDS) 130 132
50: 134 type=102 (BONDS) 130 133
50: 135 type=105 (BONDS) 134 135
50: 136 type=106 (BONDS) 134 136
50: 137 type=100 (BONDS) 136 137
50: 138 type=107 (BONDS) 136 138
50: 139 type=102 (BONDS) 138 139
50: 140 type=103 (BONDS) 138 140
50: 141 type=104 (BONDS) 138 144
50: 142 type=102 (BONDS) 140 141
50: 143 type=102 (BONDS) 140 142
50: 144 type=102 (BONDS) 140 143
50: 145 type=105 (BONDS) 144 145
50: 146 type=106 (BONDS) 144 146
50: 147 type=100 (BONDS) 146 147
50: 148 type=107 (BONDS) 146 148
50: 149 type=102 (BONDS) 148 149
50: 150 type=103 (BONDS) 148 150
50: 151 type=104 (BONDS) 148 154
50: 152 type=102 (BONDS) 150 151
50: 153 type=102 (BONDS) 150 152
50: 154 type=102 (BONDS) 150 153
50: 155 type=105 (BONDS) 154 155
50: G96Bond:
50: nr: 0
50: Morse:
50: nr: 0
50: Cubic Bonds:
50: nr: 0
50: Connect Bonds:
50: nr: 0
50: Harmonic Pot.:
50: nr: 0
50: FENE Bonds:
50: nr: 0
50: Tab. Bonds:
50: nr: 0
50: Tab. Bonds NC:
50: nr: 0
50: Restraint Pot.:
50: nr: 0
50: Angle:
50: nr: 1124
50: iatoms:
50: 0 type=116 (ANGLES) 1 0 2
50: 1 type=116 (ANGLES) 1 0 3
50: 2 type=116 (ANGLES) 1 0 4
50: 3 type=116 (ANGLES) 2 0 3
50: 4 type=116 (ANGLES) 2 0 4
50: 5 type=116 (ANGLES) 3 0 4
50: 6 type=116 (ANGLES) 0 4 5
50: 7 type=117 (ANGLES) 0 4 6
50: 8 type=117 (ANGLES) 0 4 22
50: 9 type=118 (ANGLES) 5 4 6
50: 10 type=116 (ANGLES) 5 4 22
50: 11 type=119 (ANGLES) 6 4 22
50: 12 type=118 (ANGLES) 4 6 7
50: 13 type=118 (ANGLES) 4 6 8
50: 14 type=120 (ANGLES) 4 6 9
50: 15 type=121 (ANGLES) 7 6 8
50: 16 type=118 (ANGLES) 7 6 9
50: 17 type=118 (ANGLES) 8 6 9
50: 18 type=118 (ANGLES) 6 9 10
50: 19 type=118 (ANGLES) 6 9 11
50: 20 type=120 (ANGLES) 6 9 12
50: 21 type=121 (ANGLES) 10 9 11
50: 22 type=118 (ANGLES) 10 9 12
50: 23 type=118 (ANGLES) 11 9 12
50: 24 type=118 (ANGLES) 9 12 13
50: 25 type=118 (ANGLES) 9 12 14
50: 26 type=120 (ANGLES) 9 12 15
50: 27 type=121 (ANGLES) 13 12 14
50: 28 type=118 (ANGLES) 13 12 15
50: 29 type=118 (ANGLES) 14 12 15
50: 30 type=118 (ANGLES) 12 15 16
50: 31 type=118 (ANGLES) 12 15 17
50: 32 type=117 (ANGLES) 12 15 18
50: 33 type=121 (ANGLES) 16 15 17
50: 34 type=116 (ANGLES) 16 15 18
50: 35 type=116 (ANGLES) 17 15 18
50: 36 type=116 (ANGLES) 15 18 19
50: 37 type=116 (ANGLES) 15 18 20
50: 38 type=116 (ANGLES) 15 18 21
50: 39 type=116 (ANGLES) 19 18 20
50: 40 type=116 (ANGLES) 19 18 21
50: 41 type=116 (ANGLES) 20 18 21
50: 42 type=122 (ANGLES) 4 22 23
50: 43 type=123 (ANGLES) 4 22 24
50: 44 type=124 (ANGLES) 23 22 24
50: 45 type=125 (ANGLES) 22 24 25
50: 46 type=126 (ANGLES) 22 24 26
50: 47 type=127 (ANGLES) 25 24 26
50: 48 type=116 (ANGLES) 24 26 27
50: 49 type=128 (ANGLES) 24 26 28
50: 50 type=129 (ANGLES) 24 26 38
50: 51 type=118 (ANGLES) 27 26 28
50: 52 type=116 (ANGLES) 27 26 38
50: 53 type=119 (ANGLES) 28 26 38
50: 54 type=118 (ANGLES) 26 28 29
50: 55 type=120 (ANGLES) 26 28 30
50: 56 type=120 (ANGLES) 26 28 34
50: 57 type=118 (ANGLES) 29 28 30
50: 58 type=118 (ANGLES) 29 28 34
50: 59 type=120 (ANGLES) 30 28 34
50: 60 type=118 (ANGLES) 28 30 31
50: 61 type=118 (ANGLES) 28 30 32
50: 62 type=118 (ANGLES) 28 30 33
50: 63 type=121 (ANGLES) 31 30 32
50: 64 type=121 (ANGLES) 31 30 33
50: 65 type=121 (ANGLES) 32 30 33
50: 66 type=118 (ANGLES) 28 34 35
50: 67 type=118 (ANGLES) 28 34 36
50: 68 type=118 (ANGLES) 28 34 37
50: 69 type=121 (ANGLES) 35 34 36
50: 70 type=121 (ANGLES) 35 34 37
50: 71 type=121 (ANGLES) 36 34 37
50: 72 type=122 (ANGLES) 26 38 39
50: 73 type=123 (ANGLES) 26 38 40
50: 74 type=124 (ANGLES) 39 38 40
50: 75 type=125 (ANGLES) 38 40 41
50: 76 type=126 (ANGLES) 38 40 42
50: 77 type=127 (ANGLES) 41 40 42
50: 78 type=116 (ANGLES) 40 42 43
50: 79 type=128 (ANGLES) 40 42 44
50: 80 type=129 (ANGLES) 40 42 58
50: 81 type=118 (ANGLES) 43 42 44
50: 82 type=116 (ANGLES) 43 42 58
50: 83 type=119 (ANGLES) 44 42 58
50: 84 type=118 (ANGLES) 42 44 45
50: 85 type=118 (ANGLES) 42 44 46
50: 86 type=130 (ANGLES) 42 44 47
50: 87 type=121 (ANGLES) 45 44 46
50: 88 type=116 (ANGLES) 45 44 47
50: 89 type=116 (ANGLES) 46 44 47
50: 90 type=131 (ANGLES) 44 47 48
50: 91 type=131 (ANGLES) 44 47 50
50: 92 type=132 (ANGLES) 48 47 50
50: 93 type=133 (ANGLES) 47 48 49
50: 94 type=132 (ANGLES) 47 48 52
50: 95 type=133 (ANGLES) 49 48 52
50: 96 type=133 (ANGLES) 47 50 51
50: 97 type=132 (ANGLES) 47 50 54
50: 98 type=133 (ANGLES) 51 50 54
50: 99 type=133 (ANGLES) 48 52 53
50: 100 type=132 (ANGLES) 48 52 56
50: 101 type=133 (ANGLES) 53 52 56
50: 102 type=133 (ANGLES) 50 54 55
50: 103 type=132 (ANGLES) 50 54 56
50: 104 type=133 (ANGLES) 55 54 56
50: 105 type=132 (ANGLES) 52 56 54
50: 106 type=133 (ANGLES) 52 56 57
50: 107 type=133 (ANGLES) 54 56 57
50: 108 type=122 (ANGLES) 42 58 59
50: 109 type=123 (ANGLES) 42 58 60
50: 110 type=124 (ANGLES) 59 58 60
50: 111 type=125 (ANGLES) 58 60 61
50: 112 type=126 (ANGLES) 58 60 62
50: 113 type=127 (ANGLES) 61 60 62
50: 114 type=116 (ANGLES) 60 62 63
50: 115 type=116 (ANGLES) 60 62 64
50: 116 type=129 (ANGLES) 60 62 65
50: 117 type=121 (ANGLES) 63 62 64
50: 118 type=116 (ANGLES) 63 62 65
50: 119 type=116 (ANGLES) 64 62 65
50: 120 type=122 (ANGLES) 62 65 66
50: 121 type=123 (ANGLES) 62 65 67
50: 122 type=124 (ANGLES) 66 65 67
50: 123 type=125 (ANGLES) 65 67 68
50: 124 type=126 (ANGLES) 65 67 69
50: 125 type=127 (ANGLES) 68 67 69
50: 126 type=116 (ANGLES) 67 69 70
50: 127 type=128 (ANGLES) 67 69 71
50: 128 type=129 (ANGLES) 67 69 89
50: 129 type=118 (ANGLES) 70 69 71
50: 130 type=116 (ANGLES) 70 69 89
50: 131 type=119 (ANGLES) 71 69 89
50: 132 type=118 (ANGLES) 69 71 72
50: 133 type=118 (ANGLES) 69 71 73
50: 134 type=120 (ANGLES) 69 71 74
50: 135 type=121 (ANGLES) 72 71 73
50: 136 type=118 (ANGLES) 72 71 74
50: 137 type=118 (ANGLES) 73 71 74
50: 138 type=118 (ANGLES) 71 74 75
50: 139 type=118 (ANGLES) 71 74 76
50: 140 type=120 (ANGLES) 71 74 77
50: 141 type=121 (ANGLES) 75 74 76
50: 142 type=118 (ANGLES) 75 74 77
50: 143 type=118 (ANGLES) 76 74 77
50: 144 type=118 (ANGLES) 74 77 78
50: 145 type=118 (ANGLES) 74 77 79
50: 146 type=117 (ANGLES) 74 77 80
50: 147 type=121 (ANGLES) 78 77 79
50: 148 type=116 (ANGLES) 78 77 80
50: 149 type=116 (ANGLES) 79 77 80
50: 150 type=134 (ANGLES) 77 80 81
50: 151 type=135 (ANGLES) 77 80 82
50: 152 type=133 (ANGLES) 81 80 82
50: 153 type=131 (ANGLES) 80 82 83
50: 154 type=131 (ANGLES) 80 82 86
50: 155 type=131 (ANGLES) 83 82 86
50: 156 type=133 (ANGLES) 82 83 84
50: 157 type=133 (ANGLES) 82 83 85
50: 158 type=133 (ANGLES) 84 83 85
50: 159 type=133 (ANGLES) 82 86 87
50: 160 type=133 (ANGLES) 82 86 88
50: 161 type=133 (ANGLES) 87 86 88
50: 162 type=122 (ANGLES) 69 89 90
50: 163 type=123 (ANGLES) 69 89 91
50: 164 type=124 (ANGLES) 90 89 91
50: 165 type=125 (ANGLES) 89 91 92
50: 166 type=126 (ANGLES) 89 91 93
50: 167 type=127 (ANGLES) 92 91 93
50: 168 type=116 (ANGLES) 91 93 94
50: 169 type=128 (ANGLES) 91 93 95
50: 170 type=129 (ANGLES) 91 93 100
50: 171 type=118 (ANGLES) 94 93 95
50: 172 type=116 (ANGLES) 94 93 100
50: 173 type=119 (ANGLES) 95 93 100
50: 174 type=118 (ANGLES) 93 95 96
50: 175 type=118 (ANGLES) 93 95 97
50: 176 type=136 (ANGLES) 93 95 98
50: 177 type=121 (ANGLES) 96 95 97
50: 178 type=116 (ANGLES) 96 95 98
50: 179 type=116 (ANGLES) 97 95 98
50: 180 type=137 (ANGLES) 95 98 99
50: 181 type=122 (ANGLES) 93 100 101
50: 182 type=123 (ANGLES) 93 100 102
50: 183 type=124 (ANGLES) 101 100 102
50: 184 type=125 (ANGLES) 100 102 103
50: 185 type=126 (ANGLES) 100 102 104
50: 186 type=127 (ANGLES) 103 102 104
50: 187 type=116 (ANGLES) 102 104 105
50: 188 type=128 (ANGLES) 102 104 106
50: 189 type=129 (ANGLES) 102 104 115
50: 190 type=118 (ANGLES) 105 104 106
50: 191 type=116 (ANGLES) 105 104 115
50: 192 type=119 (ANGLES) 106 104 115
50: 193 type=118 (ANGLES) 104 106 107
50: 194 type=118 (ANGLES) 104 106 108
50: 195 type=120 (ANGLES) 104 106 109
50: 196 type=121 (ANGLES) 107 106 108
50: 197 type=118 (ANGLES) 107 106 109
50: 198 type=118 (ANGLES) 108 106 109
50: 199 type=118 (ANGLES) 106 109 110
50: 200 type=118 (ANGLES) 106 109 111
50: 201 type=119 (ANGLES) 106 109 112
50: 202 type=121 (ANGLES) 110 109 111
50: 203 type=116 (ANGLES) 110 109 112
50: 204 type=116 (ANGLES) 111 109 112
50: 205 type=138 (ANGLES) 109 112 113
50: 206 type=138 (ANGLES) 109 112 114
50: 207 type=139 (ANGLES) 113 112 114
50: 208 type=122 (ANGLES) 104 115 116
50: 209 type=123 (ANGLES) 104 115 117
50: 210 type=124 (ANGLES) 116 115 117
50: 211 type=125 (ANGLES) 115 117 118
50: 212 type=126 (ANGLES) 115 117 119
50: 213 type=127 (ANGLES) 118 117 119
50: 214 type=116 (ANGLES) 117 119 120
50: 215 type=128 (ANGLES) 117 119 121
50: 216 type=129 (ANGLES) 117 119 134
50: 217 type=118 (ANGLES) 120 119 121
50: 218 type=116 (ANGLES) 120 119 134
50: 219 type=119 (ANGLES) 121 119 134
50: 220 type=118 (ANGLES) 119 121 122
50: 221 type=118 (ANGLES) 119 121 123
50: 222 type=120 (ANGLES) 119 121 124
50: 223 type=121 (ANGLES) 122 121 123
50: 224 type=118 (ANGLES) 122 121 124
50: 225 type=118 (ANGLES) 123 121 124
50: 226 type=118 (ANGLES) 121 124 125
50: 227 type=120 (ANGLES) 121 124 126
50: 228 type=120 (ANGLES) 121 124 130
50: 229 type=118 (ANGLES) 125 124 126
50: 230 type=118 (ANGLES) 125 124 130
50: 231 type=120 (ANGLES) 126 124 130
50: 232 type=118 (ANGLES) 124 126 127
50: 233 type=118 (ANGLES) 124 126 128
50: 234 type=118 (ANGLES) 124 126 129
50: 235 type=121 (ANGLES) 127 126 128
50: 236 type=121 (ANGLES) 127 126 129
50: 237 type=121 (ANGLES) 128 126 129
50: 238 type=118 (ANGLES) 124 130 131
50: 239 type=118 (ANGLES) 124 130 132
50: 240 type=118 (ANGLES) 124 130 133
50: 241 type=121 (ANGLES) 131 130 132
50: 242 type=121 (ANGLES) 131 130 133
50: 243 type=121 (ANGLES) 132 130 133
50: 244 type=122 (ANGLES) 119 134 135
50: 245 type=123 (ANGLES) 119 134 136
50: 246 type=124 (ANGLES) 135 134 136
50: 247 type=125 (ANGLES) 134 136 137
50: 248 type=126 (ANGLES) 134 136 138
50: 249 type=127 (ANGLES) 137 136 138
50: 250 type=116 (ANGLES) 136 138 139
50: 251 type=128 (ANGLES) 136 138 140
50: 252 type=129 (ANGLES) 136 138 144
50: 253 type=118 (ANGLES) 139 138 140
50: 254 type=116 (ANGLES) 139 138 144
50: 255 type=119 (ANGLES) 140 138 144
50: 256 type=118 (ANGLES) 138 140 141
50: 257 type=118 (ANGLES) 138 140 142
50: 258 type=118 (ANGLES) 138 140 143
50: 259 type=121 (ANGLES) 141 140 142
50: 260 type=121 (ANGLES) 141 140 143
50: 261 type=121 (ANGLES) 142 140 143
50: 262 type=122 (ANGLES) 138 144 145
50: 263 type=123 (ANGLES) 138 144 146
50: 264 type=124 (ANGLES) 145 144 146
50: 265 type=125 (ANGLES) 144 146 147
50: 266 type=126 (ANGLES) 144 146 148
50: 267 type=127 (ANGLES) 147 146 148
50: 268 type=116 (ANGLES) 146 148 149
50: 269 type=128 (ANGLES) 146 148 150
50: 270 type=129 (ANGLES) 146 148 154
50: 271 type=118 (ANGLES) 149 148 150
50: 272 type=116 (ANGLES) 149 148 154
50: 273 type=119 (ANGLES) 150 148 154
50: 274 type=118 (ANGLES) 148 150 151
50: 275 type=118 (ANGLES) 148 150 152
50: 276 type=118 (ANGLES) 148 150 153
50: 277 type=121 (ANGLES) 151 150 152
50: 278 type=121 (ANGLES) 151 150 153
50: 279 type=121 (ANGLES) 152 150 153
50: 280 type=122 (ANGLES) 148 154 155
50: G96Angle:
50: nr: 0
50: Restricted Angles:
50: nr: 0
50: Lin. Angle:
50: nr: 0
50: Bond-Cross:
50: nr: 0
50: BA-Cross:
50: nr: 0
50: U-B:
50: nr: 0
50: Quartic Angles:
50: nr: 0
50: Tab. Angles:
50: nr: 0
50: Proper Dih.:
50: nr: 145
50: iatoms:
50: 0 type=140 (PDIHS) 4 24 22 23
50: 1 type=141 (PDIHS) 22 26 24 25
50: 2 type=140 (PDIHS) 26 40 38 39
50: 3 type=141 (PDIHS) 38 42 40 41
50: 4 type=140 (PDIHS) 42 60 58 59
50: 5 type=142 (PDIHS) 44 47 50 48
50: 6 type=142 (PDIHS) 47 52 48 49
50: 7 type=142 (PDIHS) 47 54 50 51
50: 8 type=142 (PDIHS) 48 56 52 53
50: 9 type=142 (PDIHS) 50 56 54 55
50: 10 type=142 (PDIHS) 52 54 56 57
50: 11 type=141 (PDIHS) 58 62 60 61
50: 12 type=140 (PDIHS) 62 67 65 66
50: 13 type=141 (PDIHS) 65 69 67 68
50: 14 type=140 (PDIHS) 69 91 89 90
50: 15 type=141 (PDIHS) 77 82 80 81
50: 16 type=140 (PDIHS) 80 83 82 86
50: 17 type=141 (PDIHS) 82 84 83 85
50: 18 type=141 (PDIHS) 82 87 86 88
50: 19 type=141 (PDIHS) 89 93 91 92
50: 20 type=140 (PDIHS) 93 102 100 101
50: 21 type=141 (PDIHS) 100 104 102 103
50: 22 type=140 (PDIHS) 104 117 115 116
50: 23 type=140 (PDIHS) 109 113 112 114
50: 24 type=141 (PDIHS) 115 119 117 118
50: 25 type=140 (PDIHS) 119 136 134 135
50: 26 type=141 (PDIHS) 134 138 136 137
50: 27 type=140 (PDIHS) 138 146 144 145
50: 28 type=141 (PDIHS) 144 148 146 147
50: Ryckaert-Bell.:
50: nr: 1565
50: iatoms:
50: 0 type=143 (RBDIHS) 1 0 4 5
50: 1 type=144 (RBDIHS) 1 0 4 6
50: 2 type=144 (RBDIHS) 1 0 4 22
50: 3 type=143 (RBDIHS) 2 0 4 5
50: 4 type=144 (RBDIHS) 2 0 4 6
50: 5 type=144 (RBDIHS) 2 0 4 22
50: 6 type=143 (RBDIHS) 3 0 4 5
50: 7 type=144 (RBDIHS) 3 0 4 6
50: 8 type=144 (RBDIHS) 3 0 4 22
50: 9 type=145 (RBDIHS) 0 4 6 9
50: 10 type=146 (RBDIHS) 22 4 6 9
50: 11 type=147 (RBDIHS) 0 4 6 7
50: 12 type=147 (RBDIHS) 0 4 6 8
50: 13 type=148 (RBDIHS) 5 4 6 7
50: 14 type=148 (RBDIHS) 5 4 6 8
50: 15 type=148 (RBDIHS) 5 4 6 9
50: 16 type=149 (RBDIHS) 22 4 6 7
50: 17 type=149 (RBDIHS) 22 4 6 8
50: 18 type=150 (RBDIHS) 0 4 22 24
50: 19 type=151 (RBDIHS) 6 4 22 24
50: 20 type=148 (RBDIHS) 4 6 9 10
50: 21 type=148 (RBDIHS) 4 6 9 11
50: 22 type=152 (RBDIHS) 4 6 9 12
50: 23 type=148 (RBDIHS) 7 6 9 10
50: 24 type=148 (RBDIHS) 7 6 9 11
50: 25 type=148 (RBDIHS) 7 6 9 12
50: 26 type=148 (RBDIHS) 8 6 9 10
50: 27 type=148 (RBDIHS) 8 6 9 11
50: 28 type=148 (RBDIHS) 8 6 9 12
50: 29 type=148 (RBDIHS) 6 9 12 13
50: 30 type=148 (RBDIHS) 6 9 12 14
50: 31 type=152 (RBDIHS) 6 9 12 15
50: 32 type=148 (RBDIHS) 10 9 12 13
50: 33 type=148 (RBDIHS) 10 9 12 14
50: 34 type=148 (RBDIHS) 10 9 12 15
50: 35 type=148 (RBDIHS) 11 9 12 13
50: 36 type=148 (RBDIHS) 11 9 12 14
50: 37 type=148 (RBDIHS) 11 9 12 15
50: 38 type=148 (RBDIHS) 9 12 15 16
50: 39 type=148 (RBDIHS) 9 12 15 17
50: 40 type=153 (RBDIHS) 9 12 15 18
50: 41 type=148 (RBDIHS) 13 12 15 16
50: 42 type=148 (RBDIHS) 13 12 15 17
50: 43 type=154 (RBDIHS) 13 12 15 18
50: 44 type=148 (RBDIHS) 14 12 15 16
50: 45 type=148 (RBDIHS) 14 12 15 17
50: 46 type=154 (RBDIHS) 14 12 15 18
50: 47 type=144 (RBDIHS) 12 15 18 19
50: 48 type=144 (RBDIHS) 12 15 18 20
50: 49 type=144 (RBDIHS) 12 15 18 21
50: 50 type=143 (RBDIHS) 16 15 18 19
50: 51 type=143 (RBDIHS) 16 15 18 20
50: 52 type=143 (RBDIHS) 16 15 18 21
50: 53 type=143 (RBDIHS) 17 15 18 19
50: 54 type=143 (RBDIHS) 17 15 18 20
50: 55 type=143 (RBDIHS) 17 15 18 21
50: 56 type=155 (RBDIHS) 4 22 24 25
50: 57 type=156 (RBDIHS) 4 22 24 26
50: 58 type=155 (RBDIHS) 23 22 24 25
50: 59 type=157 (RBDIHS) 23 22 24 26
50: 60 type=158 (RBDIHS) 22 24 26 28
50: 61 type=159 (RBDIHS) 22 24 26 38
50: 62 type=160 (RBDIHS) 24 26 28 30
50: 63 type=160 (RBDIHS) 24 26 28 34
50: 64 type=161 (RBDIHS) 38 26 28 30
50: 65 type=161 (RBDIHS) 38 26 28 34
50: 66 type=147 (RBDIHS) 24 26 28 29
50: 67 type=148 (RBDIHS) 27 26 28 29
50: 68 type=148 (RBDIHS) 27 26 28 30
50: 69 type=148 (RBDIHS) 27 26 28 34
50: 70 type=149 (RBDIHS) 38 26 28 29
50: 71 type=150 (RBDIHS) 24 26 38 40
50: 72 type=151 (RBDIHS) 28 26 38 40
50: 73 type=148 (RBDIHS) 26 28 30 31
50: 74 type=148 (RBDIHS) 26 28 30 32
50: 75 type=148 (RBDIHS) 26 28 30 33
50: 76 type=148 (RBDIHS) 29 28 30 31
50: 77 type=148 (RBDIHS) 29 28 30 32
50: 78 type=148 (RBDIHS) 29 28 30 33
50: 79 type=148 (RBDIHS) 34 28 30 31
50: 80 type=148 (RBDIHS) 34 28 30 32
50: 81 type=148 (RBDIHS) 34 28 30 33
50: 82 type=148 (RBDIHS) 26 28 34 35
50: 83 type=148 (RBDIHS) 26 28 34 36
50: 84 type=148 (RBDIHS) 26 28 34 37
50: 85 type=148 (RBDIHS) 29 28 34 35
50: 86 type=148 (RBDIHS) 29 28 34 36
50: 87 type=148 (RBDIHS) 29 28 34 37
50: 88 type=148 (RBDIHS) 30 28 34 35
50: 89 type=148 (RBDIHS) 30 28 34 36
50: 90 type=148 (RBDIHS) 30 28 34 37
50: 91 type=155 (RBDIHS) 26 38 40 41
50: 92 type=156 (RBDIHS) 26 38 40 42
50: 93 type=155 (RBDIHS) 39 38 40 41
50: 94 type=157 (RBDIHS) 39 38 40 42
50: 95 type=158 (RBDIHS) 38 40 42 44
50: 96 type=159 (RBDIHS) 38 40 42 58
50: 97 type=147 (RBDIHS) 40 42 44 45
50: 98 type=147 (RBDIHS) 40 42 44 46
50: 99 type=162 (RBDIHS) 40 42 44 47
50: 100 type=148 (RBDIHS) 43 42 44 45
50: 101 type=148 (RBDIHS) 43 42 44 46
50: 102 type=163 (RBDIHS) 43 42 44 47
50: 103 type=149 (RBDIHS) 58 42 44 45
50: 104 type=149 (RBDIHS) 58 42 44 46
50: 105 type=164 (RBDIHS) 58 42 44 47
50: 106 type=150 (RBDIHS) 40 42 58 60
50: 107 type=151 (RBDIHS) 44 42 58 60
50: 108 type=165 (RBDIHS) 44 47 48 49
50: 109 type=165 (RBDIHS) 44 47 48 52
50: 110 type=165 (RBDIHS) 50 47 48 49
50: 111 type=165 (RBDIHS) 50 47 48 52
50: 112 type=165 (RBDIHS) 44 47 50 51
50: 113 type=165 (RBDIHS) 44 47 50 54
50: 114 type=165 (RBDIHS) 48 47 50 51
50: 115 type=165 (RBDIHS) 48 47 50 54
50: 116 type=165 (RBDIHS) 47 48 52 53
50: 117 type=165 (RBDIHS) 47 48 52 56
50: 118 type=165 (RBDIHS) 49 48 52 53
50: 119 type=165 (RBDIHS) 49 48 52 56
50: 120 type=165 (RBDIHS) 47 50 54 55
50: 121 type=165 (RBDIHS) 47 50 54 56
50: 122 type=165 (RBDIHS) 51 50 54 55
50: 123 type=165 (RBDIHS) 51 50 54 56
50: 124 type=165 (RBDIHS) 48 52 56 54
50: 125 type=165 (RBDIHS) 48 52 56 57
50: 126 type=165 (RBDIHS) 53 52 56 54
50: 127 type=165 (RBDIHS) 53 52 56 57
50: 128 type=165 (RBDIHS) 50 54 56 52
50: 129 type=165 (RBDIHS) 50 54 56 57
50: 130 type=165 (RBDIHS) 55 54 56 52
50: 131 type=165 (RBDIHS) 55 54 56 57
50: 132 type=155 (RBDIHS) 42 58 60 61
50: 133 type=156 (RBDIHS) 42 58 60 62
50: 134 type=155 (RBDIHS) 59 58 60 61
50: 135 type=157 (RBDIHS) 59 58 60 62
50: 136 type=159 (RBDIHS) 58 60 62 65
50: 137 type=150 (RBDIHS) 60 62 65 67
50: 138 type=155 (RBDIHS) 62 65 67 68
50: 139 type=156 (RBDIHS) 62 65 67 69
50: 140 type=155 (RBDIHS) 66 65 67 68
50: 141 type=157 (RBDIHS) 66 65 67 69
50: 142 type=158 (RBDIHS) 65 67 69 71
50: 143 type=159 (RBDIHS) 65 67 69 89
50: 144 type=166 (RBDIHS) 67 69 71 74
50: 145 type=167 (RBDIHS) 89 69 71 74
50: 146 type=147 (RBDIHS) 67 69 71 72
50: 147 type=147 (RBDIHS) 67 69 71 73
50: 148 type=148 (RBDIHS) 70 69 71 72
50: 149 type=148 (RBDIHS) 70 69 71 73
50: 150 type=148 (RBDIHS) 70 69 71 74
50: 151 type=149 (RBDIHS) 89 69 71 72
50: 152 type=149 (RBDIHS) 89 69 71 73
50: 153 type=150 (RBDIHS) 67 69 89 91
50: 154 type=151 (RBDIHS) 71 69 89 91
50: 155 type=148 (RBDIHS) 69 71 74 75
50: 156 type=148 (RBDIHS) 69 71 74 76
50: 157 type=152 (RBDIHS) 69 71 74 77
50: 158 type=148 (RBDIHS) 72 71 74 75
50: 159 type=148 (RBDIHS) 72 71 74 76
50: 160 type=148 (RBDIHS) 72 71 74 77
50: 161 type=148 (RBDIHS) 73 71 74 75
50: 162 type=148 (RBDIHS) 73 71 74 76
50: 163 type=148 (RBDIHS) 73 71 74 77
50: 164 type=148 (RBDIHS) 71 74 77 78
50: 165 type=148 (RBDIHS) 71 74 77 79
50: 166 type=153 (RBDIHS) 71 74 77 80
50: 167 type=148 (RBDIHS) 75 74 77 78
50: 168 type=148 (RBDIHS) 75 74 77 79
50: 169 type=168 (RBDIHS) 75 74 77 80
50: 170 type=148 (RBDIHS) 76 74 77 78
50: 171 type=148 (RBDIHS) 76 74 77 79
50: 172 type=168 (RBDIHS) 76 74 77 80
50: 173 type=169 (RBDIHS) 74 77 80 81
50: 174 type=170 (RBDIHS) 74 77 80 82
50: 175 type=171 (RBDIHS) 78 77 80 82
50: 176 type=171 (RBDIHS) 79 77 80 82
50: 177 type=172 (RBDIHS) 77 80 82 83
50: 178 type=172 (RBDIHS) 77 80 82 86
50: 179 type=173 (RBDIHS) 81 80 82 83
50: 180 type=173 (RBDIHS) 81 80 82 86
50: 181 type=173 (RBDIHS) 80 82 83 84
50: 182 type=173 (RBDIHS) 80 82 83 85
50: 183 type=173 (RBDIHS) 86 82 83 84
50: 184 type=173 (RBDIHS) 86 82 83 85
50: 185 type=173 (RBDIHS) 80 82 86 87
50: 186 type=173 (RBDIHS) 80 82 86 88
50: 187 type=173 (RBDIHS) 83 82 86 87
50: 188 type=173 (RBDIHS) 83 82 86 88
50: 189 type=155 (RBDIHS) 69 89 91 92
50: 190 type=156 (RBDIHS) 69 89 91 93
50: 191 type=155 (RBDIHS) 90 89 91 92
50: 192 type=157 (RBDIHS) 90 89 91 93
50: 193 type=158 (RBDIHS) 89 91 93 95
50: 194 type=159 (RBDIHS) 89 91 93 100
50: 195 type=174 (RBDIHS) 91 93 95 98
50: 196 type=175 (RBDIHS) 100 93 95 98
50: 197 type=147 (RBDIHS) 91 93 95 96
50: 198 type=147 (RBDIHS) 91 93 95 97
50: 199 type=148 (RBDIHS) 94 93 95 96
50: 200 type=148 (RBDIHS) 94 93 95 97
50: 201 type=176 (RBDIHS) 94 93 95 98
50: 202 type=149 (RBDIHS) 100 93 95 96
50: 203 type=149 (RBDIHS) 100 93 95 97
50: 204 type=150 (RBDIHS) 91 93 100 102
50: 205 type=151 (RBDIHS) 95 93 100 102
50: 206 type=177 (RBDIHS) 93 95 98 99
50: 207 type=178 (RBDIHS) 96 95 98 99
50: 208 type=178 (RBDIHS) 97 95 98 99
50: 209 type=155 (RBDIHS) 93 100 102 103
50: 210 type=156 (RBDIHS) 93 100 102 104
50: 211 type=155 (RBDIHS) 101 100 102 103
50: 212 type=157 (RBDIHS) 101 100 102 104
50: 213 type=158 (RBDIHS) 100 102 104 106
50: 214 type=159 (RBDIHS) 100 102 104 115
50: 215 type=179 (RBDIHS) 102 104 106 109
50: 216 type=180 (RBDIHS) 115 104 106 109
50: 217 type=147 (RBDIHS) 102 104 106 107
50: 218 type=147 (RBDIHS) 102 104 106 108
50: 219 type=148 (RBDIHS) 105 104 106 107
50: 220 type=148 (RBDIHS) 105 104 106 108
50: 221 type=148 (RBDIHS) 105 104 106 109
50: 222 type=149 (RBDIHS) 115 104 106 107
50: 223 type=149 (RBDIHS) 115 104 106 108
50: 224 type=150 (RBDIHS) 102 104 115 117
50: 225 type=151 (RBDIHS) 106 104 115 117
50: 226 type=148 (RBDIHS) 104 106 109 110
50: 227 type=148 (RBDIHS) 104 106 109 111
50: 228 type=181 (RBDIHS) 104 106 109 112
50: 229 type=148 (RBDIHS) 107 106 109 110
50: 230 type=148 (RBDIHS) 107 106 109 111
50: 231 type=182 (RBDIHS) 107 106 109 112
50: 232 type=148 (RBDIHS) 108 106 109 110
50: 233 type=148 (RBDIHS) 108 106 109 111
50: 234 type=182 (RBDIHS) 108 106 109 112
50: 235 type=183 (RBDIHS) 106 109 112 113
50: 236 type=183 (RBDIHS) 106 109 112 114
50: 237 type=155 (RBDIHS) 104 115 117 118
50: 238 type=156 (RBDIHS) 104 115 117 119
50: 239 type=155 (RBDIHS) 116 115 117 118
50: 240 type=157 (RBDIHS) 116 115 117 119
50: 241 type=158 (RBDIHS) 115 117 119 121
50: 242 type=159 (RBDIHS) 115 117 119 134
50: 243 type=184 (RBDIHS) 117 119 121 124
50: 244 type=185 (RBDIHS) 134 119 121 124
50: 245 type=147 (RBDIHS) 117 119 121 122
50: 246 type=147 (RBDIHS) 117 119 121 123
50: 247 type=148 (RBDIHS) 120 119 121 122
50: 248 type=148 (RBDIHS) 120 119 121 123
50: 249 type=148 (RBDIHS) 120 119 121 124
50: 250 type=149 (RBDIHS) 134 119 121 122
50: 251 type=149 (RBDIHS) 134 119 121 123
50: 252 type=150 (RBDIHS) 117 119 134 136
50: 253 type=151 (RBDIHS) 121 119 134 136
50: 254 type=148 (RBDIHS) 119 121 124 125
50: 255 type=152 (RBDIHS) 119 121 124 126
50: 256 type=152 (RBDIHS) 119 121 124 130
50: 257 type=148 (RBDIHS) 122 121 124 125
50: 258 type=148 (RBDIHS) 122 121 124 126
50: 259 type=148 (RBDIHS) 122 121 124 130
50: 260 type=148 (RBDIHS) 123 121 124 125
50: 261 type=148 (RBDIHS) 123 121 124 126
50: 262 type=148 (RBDIHS) 123 121 124 130
50: 263 type=148 (RBDIHS) 121 124 126 127
50: 264 type=148 (RBDIHS) 121 124 126 128
50: 265 type=148 (RBDIHS) 121 124 126 129
50: 266 type=148 (RBDIHS) 125 124 126 127
50: 267 type=148 (RBDIHS) 125 124 126 128
50: 268 type=148 (RBDIHS) 125 124 126 129
50: 269 type=148 (RBDIHS) 130 124 126 127
50: 270 type=148 (RBDIHS) 130 124 126 128
50: 271 type=148 (RBDIHS) 130 124 126 129
50: 272 type=148 (RBDIHS) 121 124 130 131
50: 273 type=148 (RBDIHS) 121 124 130 132
50: 274 type=148 (RBDIHS) 121 124 130 133
50: 275 type=148 (RBDIHS) 125 124 130 131
50: 276 type=148 (RBDIHS) 125 124 130 132
50: 277 type=148 (RBDIHS) 125 124 130 133
50: 278 type=148 (RBDIHS) 126 124 130 131
50: 279 type=148 (RBDIHS) 126 124 130 132
50: 280 type=148 (RBDIHS) 126 124 130 133
50: 281 type=155 (RBDIHS) 119 134 136 137
50: 282 type=156 (RBDIHS) 119 134 136 138
50: 283 type=155 (RBDIHS) 135 134 136 137
50: 284 type=157 (RBDIHS) 135 134 136 138
50: 285 type=158 (RBDIHS) 134 136 138 140
50: 286 type=159 (RBDIHS) 134 136 138 144
50: 287 type=147 (RBDIHS) 136 138 140 141
50: 288 type=147 (RBDIHS) 136 138 140 142
50: 289 type=147 (RBDIHS) 136 138 140 143
50: 290 type=148 (RBDIHS) 139 138 140 141
50: 291 type=148 (RBDIHS) 139 138 140 142
50: 292 type=148 (RBDIHS) 139 138 140 143
50: 293 type=149 (RBDIHS) 144 138 140 141
50: 294 type=149 (RBDIHS) 144 138 140 142
50: 295 type=149 (RBDIHS) 144 138 140 143
50: 296 type=150 (RBDIHS) 136 138 144 146
50: 297 type=151 (RBDIHS) 140 138 144 146
50: 298 type=155 (RBDIHS) 138 144 146 147
50: 299 type=156 (RBDIHS) 138 144 146 148
50: 300 type=155 (RBDIHS) 145 144 146 147
50: 301 type=157 (RBDIHS) 145 144 146 148
50: 302 type=158 (RBDIHS) 144 146 148 150
50: 303 type=159 (RBDIHS) 144 146 148 154
50: 304 type=147 (RBDIHS) 146 148 150 151
50: 305 type=147 (RBDIHS) 146 148 150 152
50: 306 type=147 (RBDIHS) 146 148 150 153
50: 307 type=148 (RBDIHS) 149 148 150 151
50: 308 type=148 (RBDIHS) 149 148 150 152
50: 309 type=148 (RBDIHS) 149 148 150 153
50: 310 type=149 (RBDIHS) 154 148 150 151
50: 311 type=149 (RBDIHS) 154 148 150 152
50: 312 type=149 (RBDIHS) 154 148 150 153
50: Restricted Dih.:
50: nr: 0
50: CBT Dih.:
50: nr: 0
50: Fourier Dih.:
50: nr: 0
50: Improper Dih.:
50: nr: 0
50: Improper Dih.:
50: nr: 0
50: Tab. Dih.:
50: nr: 0
50: CMAP Dih.:
50: nr: 0
50: GB 1-2 Pol. (unused):
50: nr: 0
50: GB 1-3 Pol. (unused):
50: nr: 0
50: GB 1-4 Pol. (unused):
50: nr: 0
50: GB Polarization (unused):
50: nr: 0
50: Nonpolar Sol. (unused):
50: nr: 0
50: LJ-14:
50: nr: 1197
50: iatoms:
50: 0 type=186 (LJ14) 0 7
50: 1 type=186 (LJ14) 0 8
50: 2 type=187 (LJ14) 0 9
50: 3 type=188 (LJ14) 0 23
50: 4 type=189 (LJ14) 0 24
50: 5 type=190 (LJ14) 1 5
50: 6 type=190 (LJ14) 1 6
50: 7 type=190 (LJ14) 1 22
50: 8 type=190 (LJ14) 2 5
50: 9 type=190 (LJ14) 2 6
50: 10 type=190 (LJ14) 2 22
50: 11 type=190 (LJ14) 3 5
50: 12 type=190 (LJ14) 3 6
50: 13 type=190 (LJ14) 3 22
50: 14 type=191 (LJ14) 4 10
50: 15 type=191 (LJ14) 4 11
50: 16 type=192 (LJ14) 4 12
50: 17 type=190 (LJ14) 4 25
50: 18 type=192 (LJ14) 4 26
50: 19 type=193 (LJ14) 5 7
50: 20 type=193 (LJ14) 5 8
50: 21 type=191 (LJ14) 5 9
50: 22 type=194 (LJ14) 5 23
50: 23 type=186 (LJ14) 5 24
50: 24 type=191 (LJ14) 6 13
50: 25 type=191 (LJ14) 6 14
50: 26 type=192 (LJ14) 6 15
50: 27 type=195 (LJ14) 6 23
50: 28 type=187 (LJ14) 6 24
50: 29 type=193 (LJ14) 7 10
50: 30 type=193 (LJ14) 7 11
50: 31 type=191 (LJ14) 7 12
50: 32 type=196 (LJ14) 7 22
50: 33 type=193 (LJ14) 8 10
50: 34 type=193 (LJ14) 8 11
50: 35 type=191 (LJ14) 8 12
50: 36 type=196 (LJ14) 8 22
50: 37 type=191 (LJ14) 9 16
50: 38 type=191 (LJ14) 9 17
50: 39 type=187 (LJ14) 9 18
50: 40 type=197 (LJ14) 9 22
50: 41 type=193 (LJ14) 10 13
50: 42 type=193 (LJ14) 10 14
50: 43 type=191 (LJ14) 10 15
50: 44 type=193 (LJ14) 11 13
50: 45 type=193 (LJ14) 11 14
50: 46 type=191 (LJ14) 11 15
50: 47 type=190 (LJ14) 12 19
50: 48 type=190 (LJ14) 12 20
50: 49 type=190 (LJ14) 12 21
50: 50 type=193 (LJ14) 13 16
50: 51 type=193 (LJ14) 13 17
50: 52 type=186 (LJ14) 13 18
50: 53 type=193 (LJ14) 14 16
50: 54 type=193 (LJ14) 14 17
50: 55 type=186 (LJ14) 14 18
50: 56 type=190 (LJ14) 16 19
50: 57 type=190 (LJ14) 16 20
50: 58 type=190 (LJ14) 16 21
50: 59 type=190 (LJ14) 17 19
50: 60 type=190 (LJ14) 17 20
50: 61 type=190 (LJ14) 17 21
50: 62 type=196 (LJ14) 22 27
50: 63 type=197 (LJ14) 22 28
50: 64 type=198 (LJ14) 22 38
50: 65 type=190 (LJ14) 23 25
50: 66 type=195 (LJ14) 23 26
50: 67 type=186 (LJ14) 24 29
50: 68 type=187 (LJ14) 24 30
50: 69 type=187 (LJ14) 24 34
50: 70 type=188 (LJ14) 24 39
50: 71 type=189 (LJ14) 24 40
50: 72 type=190 (LJ14) 25 27
50: 73 type=190 (LJ14) 25 28
50: 74 type=190 (LJ14) 25 38
50: 75 type=191 (LJ14) 26 31
50: 76 type=191 (LJ14) 26 32
50: 77 type=191 (LJ14) 26 33
50: 78 type=191 (LJ14) 26 35
50: 79 type=191 (LJ14) 26 36
50: 80 type=191 (LJ14) 26 37
50: 81 type=190 (LJ14) 26 41
50: 82 type=192 (LJ14) 26 42
50: 83 type=193 (LJ14) 27 29
50: 84 type=191 (LJ14) 27 30
50: 85 type=191 (LJ14) 27 34
50: 86 type=194 (LJ14) 27 39
50: 87 type=186 (LJ14) 27 40
50: 88 type=195 (LJ14) 28 39
50: 89 type=187 (LJ14) 28 40
50: 90 type=193 (LJ14) 29 31
50: 91 type=193 (LJ14) 29 32
50: 92 type=193 (LJ14) 29 33
50: 93 type=193 (LJ14) 29 35
50: 94 type=193 (LJ14) 29 36
50: 95 type=193 (LJ14) 29 37
50: 96 type=196 (LJ14) 29 38
50: 97 type=191 (LJ14) 30 35
50: 98 type=191 (LJ14) 30 36
50: 99 type=191 (LJ14) 30 37
50: 100 type=197 (LJ14) 30 38
50: 101 type=191 (LJ14) 31 34
50: 102 type=191 (LJ14) 32 34
50: 103 type=191 (LJ14) 33 34
50: 104 type=197 (LJ14) 34 38
50: 105 type=196 (LJ14) 38 43
50: 106 type=197 (LJ14) 38 44
50: 107 type=198 (LJ14) 38 58
50: 108 type=190 (LJ14) 39 41
50: 109 type=195 (LJ14) 39 42
50: 110 type=186 (LJ14) 40 45
50: 111 type=186 (LJ14) 40 46
50: 112 type=199 (LJ14) 40 47
50: 113 type=188 (LJ14) 40 59
50: 114 type=189 (LJ14) 40 60
50: 115 type=190 (LJ14) 41 43
50: 116 type=190 (LJ14) 41 44
50: 117 type=190 (LJ14) 41 58
50: 118 type=200 (LJ14) 42 48
50: 119 type=200 (LJ14) 42 50
50: 120 type=190 (LJ14) 42 61
50: 121 type=192 (LJ14) 42 62
50: 122 type=193 (LJ14) 43 45
50: 123 type=193 (LJ14) 43 46
50: 124 type=201 (LJ14) 43 47
50: 125 type=194 (LJ14) 43 59
50: 126 type=186 (LJ14) 43 60
50: 127 type=202 (LJ14) 44 49
50: 128 type=202 (LJ14) 44 51
50: 129 type=200 (LJ14) 44 52
50: 130 type=200 (LJ14) 44 54
50: 131 type=195 (LJ14) 44 59
50: 132 type=187 (LJ14) 44 60
50: 133 type=201 (LJ14) 45 48
50: 134 type=201 (LJ14) 45 50
50: 135 type=196 (LJ14) 45 58
50: 136 type=201 (LJ14) 46 48
50: 137 type=201 (LJ14) 46 50
50: 138 type=196 (LJ14) 46 58
50: 139 type=203 (LJ14) 47 53
50: 140 type=203 (LJ14) 47 55
50: 141 type=204 (LJ14) 47 56
50: 142 type=205 (LJ14) 47 58
50: 143 type=203 (LJ14) 48 51
50: 144 type=204 (LJ14) 48 54
50: 145 type=203 (LJ14) 48 57
50: 146 type=203 (LJ14) 49 50
50: 147 type=206 (LJ14) 49 53
50: 148 type=203 (LJ14) 49 56
50: 149 type=204 (LJ14) 50 52
50: 150 type=203 (LJ14) 50 57
50: 151 type=206 (LJ14) 51 55
50: 152 type=203 (LJ14) 51 56
50: 153 type=203 (LJ14) 52 55
50: 154 type=203 (LJ14) 53 54
50: 155 type=206 (LJ14) 53 57
50: 156 type=206 (LJ14) 55 57
50: 157 type=196 (LJ14) 58 63
50: 158 type=196 (LJ14) 58 64
50: 159 type=198 (LJ14) 58 65
50: 160 type=190 (LJ14) 59 61
50: 161 type=195 (LJ14) 59 62
50: 162 type=188 (LJ14) 60 66
50: 163 type=189 (LJ14) 60 67
50: 164 type=190 (LJ14) 61 63
50: 165 type=190 (LJ14) 61 64
50: 166 type=190 (LJ14) 61 65
50: 167 type=190 (LJ14) 62 68
50: 168 type=192 (LJ14) 62 69
50: 169 type=194 (LJ14) 63 66
50: 170 type=186 (LJ14) 63 67
50: 171 type=194 (LJ14) 64 66
50: 172 type=186 (LJ14) 64 67
50: 173 type=196 (LJ14) 65 70
50: 174 type=197 (LJ14) 65 71
50: 175 type=198 (LJ14) 65 89
50: 176 type=190 (LJ14) 66 68
50: 177 type=195 (LJ14) 66 69
50: 178 type=186 (LJ14) 67 72
50: 179 type=186 (LJ14) 67 73
50: 180 type=187 (LJ14) 67 74
50: 181 type=188 (LJ14) 67 90
50: 182 type=189 (LJ14) 67 91
50: 183 type=190 (LJ14) 68 70
50: 184 type=190 (LJ14) 68 71
50: 185 type=190 (LJ14) 68 89
50: 186 type=191 (LJ14) 69 75
50: 187 type=191 (LJ14) 69 76
50: 188 type=192 (LJ14) 69 77
50: 189 type=190 (LJ14) 69 92
50: 190 type=192 (LJ14) 69 93
50: 191 type=193 (LJ14) 70 72
50: 192 type=193 (LJ14) 70 73
50: 193 type=191 (LJ14) 70 74
50: 194 type=194 (LJ14) 70 90
50: 195 type=186 (LJ14) 70 91
50: 196 type=191 (LJ14) 71 78
50: 197 type=191 (LJ14) 71 79
50: 198 type=187 (LJ14) 71 80
50: 199 type=195 (LJ14) 71 90
50: 200 type=187 (LJ14) 71 91
50: 201 type=193 (LJ14) 72 75
50: 202 type=193 (LJ14) 72 76
50: 203 type=191 (LJ14) 72 77
50: 204 type=196 (LJ14) 72 89
50: 205 type=193 (LJ14) 73 75
50: 206 type=193 (LJ14) 73 76
50: 207 type=191 (LJ14) 73 77
50: 208 type=196 (LJ14) 73 89
50: 209 type=190 (LJ14) 74 81
50: 210 type=207 (LJ14) 74 82
50: 211 type=197 (LJ14) 74 89
50: 212 type=193 (LJ14) 75 78
50: 213 type=193 (LJ14) 75 79
50: 214 type=186 (LJ14) 75 80
50: 215 type=193 (LJ14) 76 78
50: 216 type=193 (LJ14) 76 79
50: 217 type=186 (LJ14) 76 80
50: 218 type=187 (LJ14) 77 83
50: 219 type=187 (LJ14) 77 86
50: 220 type=190 (LJ14) 78 81
50: 221 type=208 (LJ14) 78 82
50: 222 type=190 (LJ14) 79 81
50: 223 type=208 (LJ14) 79 82
50: 224 type=190 (LJ14) 80 84
50: 225 type=190 (LJ14) 80 85
50: 226 type=190 (LJ14) 80 87
50: 227 type=190 (LJ14) 80 88
50: 228 type=190 (LJ14) 81 83
50: 229 type=190 (LJ14) 81 86
50: 230 type=190 (LJ14) 83 87
50: 231 type=190 (LJ14) 83 88
50: 232 type=190 (LJ14) 84 86
50: 233 type=190 (LJ14) 85 86
50: 234 type=196 (LJ14) 89 94
50: 235 type=197 (LJ14) 89 95
50: 236 type=198 (LJ14) 89 100
50: 237 type=190 (LJ14) 90 92
50: 238 type=195 (LJ14) 90 93
50: 239 type=186 (LJ14) 91 96
50: 240 type=186 (LJ14) 91 97
50: 241 type=209 (LJ14) 91 98
50: 242 type=188 (LJ14) 91 101
50: 243 type=189 (LJ14) 91 102
50: 244 type=190 (LJ14) 92 94
50: 245 type=190 (LJ14) 92 95
50: 246 type=190 (LJ14) 92 100
50: 247 type=190 (LJ14) 93 99
50: 248 type=190 (LJ14) 93 103
50: 249 type=192 (LJ14) 93 104
50: 250 type=193 (LJ14) 94 96
50: 251 type=193 (LJ14) 94 97
50: 252 type=210 (LJ14) 94 98
50: 253 type=194 (LJ14) 94 101
50: 254 type=186 (LJ14) 94 102
50: 255 type=195 (LJ14) 95 101
50: 256 type=187 (LJ14) 95 102
50: 257 type=190 (LJ14) 96 99
50: 258 type=196 (LJ14) 96 100
50: 259 type=190 (LJ14) 97 99
50: 260 type=196 (LJ14) 97 100
50: 261 type=211 (LJ14) 98 100
50: 262 type=196 (LJ14) 100 105
50: 263 type=197 (LJ14) 100 106
50: 264 type=198 (LJ14) 100 115
50: 265 type=190 (LJ14) 101 103
50: 266 type=195 (LJ14) 101 104
50: 267 type=186 (LJ14) 102 107
50: 268 type=186 (LJ14) 102 108
50: 269 type=187 (LJ14) 102 109
50: 270 type=188 (LJ14) 102 116
50: 271 type=189 (LJ14) 102 117
50: 272 type=190 (LJ14) 103 105
50: 273 type=190 (LJ14) 103 106
50: 274 type=190 (LJ14) 103 115
50: 275 type=191 (LJ14) 104 110
50: 276 type=191 (LJ14) 104 111
50: 277 type=197 (LJ14) 104 112
50: 278 type=190 (LJ14) 104 118
50: 279 type=192 (LJ14) 104 119
50: 280 type=193 (LJ14) 105 107
50: 281 type=193 (LJ14) 105 108
50: 282 type=191 (LJ14) 105 109
50: 283 type=194 (LJ14) 105 116
50: 284 type=186 (LJ14) 105 117
50: 285 type=195 (LJ14) 106 113
50: 286 type=195 (LJ14) 106 114
50: 287 type=195 (LJ14) 106 116
50: 288 type=187 (LJ14) 106 117
50: 289 type=193 (LJ14) 107 110
50: 290 type=193 (LJ14) 107 111
50: 291 type=196 (LJ14) 107 112
50: 292 type=196 (LJ14) 107 115
50: 293 type=193 (LJ14) 108 110
50: 294 type=193 (LJ14) 108 111
50: 295 type=196 (LJ14) 108 112
50: 296 type=196 (LJ14) 108 115
50: 297 type=197 (LJ14) 109 115
50: 298 type=194 (LJ14) 110 113
50: 299 type=194 (LJ14) 110 114
50: 300 type=194 (LJ14) 111 113
50: 301 type=194 (LJ14) 111 114
50: 302 type=196 (LJ14) 115 120
50: 303 type=197 (LJ14) 115 121
50: 304 type=198 (LJ14) 115 134
50: 305 type=190 (LJ14) 116 118
50: 306 type=195 (LJ14) 116 119
50: 307 type=186 (LJ14) 117 122
50: 308 type=186 (LJ14) 117 123
50: 309 type=187 (LJ14) 117 124
50: 310 type=188 (LJ14) 117 135
50: 311 type=189 (LJ14) 117 136
50: 312 type=190 (LJ14) 118 120
50: 313 type=190 (LJ14) 118 121
50: 314 type=190 (LJ14) 118 134
50: 315 type=191 (LJ14) 119 125
50: 316 type=192 (LJ14) 119 126
50: 317 type=192 (LJ14) 119 130
50: 318 type=190 (LJ14) 119 137
50: 319 type=192 (LJ14) 119 138
50: 320 type=193 (LJ14) 120 122
50: 321 type=193 (LJ14) 120 123
50: 322 type=191 (LJ14) 120 124
50: 323 type=194 (LJ14) 120 135
50: 324 type=186 (LJ14) 120 136
50: 325 type=191 (LJ14) 121 127
50: 326 type=191 (LJ14) 121 128
50: 327 type=191 (LJ14) 121 129
50: 328 type=191 (LJ14) 121 131
50: 329 type=191 (LJ14) 121 132
50: 330 type=191 (LJ14) 121 133
50: 331 type=195 (LJ14) 121 135
50: 332 type=187 (LJ14) 121 136
50: 333 type=193 (LJ14) 122 125
50: 334 type=191 (LJ14) 122 126
50: 335 type=191 (LJ14) 122 130
50: 336 type=196 (LJ14) 122 134
50: 337 type=193 (LJ14) 123 125
50: 338 type=191 (LJ14) 123 126
50: 339 type=191 (LJ14) 123 130
50: 340 type=196 (LJ14) 123 134
50: 341 type=197 (LJ14) 124 134
50: 342 type=193 (LJ14) 125 127
50: 343 type=193 (LJ14) 125 128
50: 344 type=193 (LJ14) 125 129
50: 345 type=193 (LJ14) 125 131
50: 346 type=193 (LJ14) 125 132
50: 347 type=193 (LJ14) 125 133
50: 348 type=191 (LJ14) 126 131
50: 349 type=191 (LJ14) 126 132
50: 350 type=191 (LJ14) 126 133
50: 351 type=191 (LJ14) 127 130
50: 352 type=191 (LJ14) 128 130
50: 353 type=191 (LJ14) 129 130
50: 354 type=196 (LJ14) 134 139
50: 355 type=197 (LJ14) 134 140
50: 356 type=198 (LJ14) 134 144
50: 357 type=190 (LJ14) 135 137
50: 358 type=195 (LJ14) 135 138
50: 359 type=186 (LJ14) 136 141
50: 360 type=186 (LJ14) 136 142
50: 361 type=186 (LJ14) 136 143
50: 362 type=188 (LJ14) 136 145
50: 363 type=189 (LJ14) 136 146
50: 364 type=190 (LJ14) 137 139
50: 365 type=190 (LJ14) 137 140
50: 366 type=190 (LJ14) 137 144
50: 367 type=190 (LJ14) 138 147
50: 368 type=192 (LJ14) 138 148
50: 369 type=193 (LJ14) 139 141
50: 370 type=193 (LJ14) 139 142
50: 371 type=193 (LJ14) 139 143
50: 372 type=194 (LJ14) 139 145
50: 373 type=186 (LJ14) 139 146
50: 374 type=195 (LJ14) 140 145
50: 375 type=187 (LJ14) 140 146
50: 376 type=196 (LJ14) 141 144
50: 377 type=196 (LJ14) 142 144
50: 378 type=196 (LJ14) 143 144
50: 379 type=196 (LJ14) 144 149
50: 380 type=197 (LJ14) 144 150
50: 381 type=198 (LJ14) 144 154
50: 382 type=190 (LJ14) 145 147
50: 383 type=195 (LJ14) 145 148
50: 384 type=186 (LJ14) 146 151
50: 385 type=186 (LJ14) 146 152
50: 386 type=186 (LJ14) 146 153
50: 387 type=188 (LJ14) 146 155
50: 388 type=190 (LJ14) 147 149
50: 389 type=190 (LJ14) 147 150
50: 390 type=190 (LJ14) 147 154
50: 391 type=193 (LJ14) 149 151
50: 392 type=193 (LJ14) 149 152
50: 393 type=193 (LJ14) 149 153
50: 394 type=194 (LJ14) 149 155
50: 395 type=195 (LJ14) 150 155
50: 396 type=196 (LJ14) 151 154
50: 397 type=196 (LJ14) 152 154
50: 398 type=196 (LJ14) 153 154
50: Coulomb-14:
50: nr: 0
50: LJC-14 q:
50: nr: 0
50: LJC Pairs NB:
50: nr: 0
50: LJ (SR):
50: nr: 0
50: Buck.ham (SR):
50: nr: 0
50: LJ (unused):
50: nr: 0
50: B.ham (unused):
50: nr: 0
50: Disper. corr.:
50: nr: 0
50: Coulomb (SR):
50: nr: 0
50: Coul (unused):
50: nr: 0
50: RF excl.:
50: nr: 0
50: Coul. recip.:
50: nr: 0
50: LJ recip.:
50: nr: 0
50: DPD:
50: nr: 0
50: Polarization:
50: nr: 0
50: Water Pol.:
50: nr: 0
50: Thole Pol.:
50: nr: 0
50: Anharm. Pol.:
50: nr: 0
50: Position Rest.:
50: nr: 0
50: Flat-bottom posres:
50: nr: 0
50: Dis. Rest.:
50: nr: 0
50: D.R.Viol. (nm):
50: nr: 0
50: Orient. Rest.:
50: nr: 0
50: Ori. R. RMSD:
50: nr: 0
50: Angle Rest.:
50: nr: 0
50: Angle Rest. Z:
50: nr: 0
50: Dih. Rest.:
50: nr: 0
50: Dih. Rest. Viol.:
50: nr: 0
50: Constraint:
50: nr: 0
50: Constr. No Conn.:
50: nr: 0
50: Settle:
50: nr: 0
50: Virtual site 1:
50: nr: 0
50: Virtual site 2:
50: nr: 0
50: Virtual site 2fd:
50: nr: 0
50: Virtual site 3:
50: nr: 0
50: Virtual site 3fd:
50: nr: 0
50: Virtual site 3fad:
50: nr: 0
50: Virtual site 3out:
50: nr: 0
50: Virtual site 4fd:
50: nr: 0
50: Virtual site 4fdn:
50: nr: 0
50: Virtual site N:
50: nr: 0
50: COM Pull En.:
50: nr: 0
50: Density fitting:
50: nr: 0
50: Quantum En.:
50: nr: 0
50: Potential:
50: nr: 0
50: Kinetic En.:
50: nr: 0
50: Total Energy:
50: nr: 0
50: Conserved En.:
50: nr: 0
50: Temperature:
50: nr: 0
50: Vir. Temp. (not used):
50: nr: 0
50: Pres. DC:
50: nr: 0
50: Pressure:
50: nr: 0
50: dH/dl constr.:
50: nr: 0
50: dVremain/dl:
50: nr: 0
50: dEkin/dl:
50: nr: 0
50: dVcoul/dl:
50: nr: 0
50: dVvdw/dl:
50: nr: 0
50: dVbonded/dl:
50: nr: 0
50: dVrestraint/dl:
50: nr: 0
50: dVtemperature/dl:
50: nr: 0
50: grp[T-Coupling ] nr=1, name=[ rest]
50: grp[Energy Mon. ] nr=1, name=[ rest]
50: grp[Acceleration] nr=1, name=[ rest]
50: grp[Freeze ] nr=1, name=[ rest]
50: grp[User1 ] nr=1, name=[ rest]
50: grp[User2 ] nr=1, name=[ rest]
50: grp[VCM ] nr=1, name=[ rest]
50: grp[Compressed X] nr=1, name=[ rest]
50: grp[Or. Res. Fit] nr=1, name=[ rest]
50: grp[QMMM ] nr=1, name=[ rest]
50: grpname (11):
50: grpname[0]={name="System"}
50: grpname[1]={name="Protein"}
50: grpname[2]={name="Protein-H"}
50: grpname[3]={name="C-alpha"}
50: grpname[4]={name="Backbone"}
50: grpname[5]={name="MainChain"}
50: grpname[6]={name="MainChain+Cb"}
50: grpname[7]={name="MainChain+H"}
50: grpname[8]={name="SideChain"}
50: grpname[9]={name="SideChain-H"}
50: grpname[10]={name="rest"}
50: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
50: allocated 0 0 0 0 0 0 0 0 0 0
50: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
50: box (3x3):
50: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
50: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
50: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
50: box_rel (3x3):
50: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv (3x3):
50: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev (3x3):
50: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev (3x3):
50: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev (3x3):
50: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: nosehoover_xi: not available
50: x (156x3):
50: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
50: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
50: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
50: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
50: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
50: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
50: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
50: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
50: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
50: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
50: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
50: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
50: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
50: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
50: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
50: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
50: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
50: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
50: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
50: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
50: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
50: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
50: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
50: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
50: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
50: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
50: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
50: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
50: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
50: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
50: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
50: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
50: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
50: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
50: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
50: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
50: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
50: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
50: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
50: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
50: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
50: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
50: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
50: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
50: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
50: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
50: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
50: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
50: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
50: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
50: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
50: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
50: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
50: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
50: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
50: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
50: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
50: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
50: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
50: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
50: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
50: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
50: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
50: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
50: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
50: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
50: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
50: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
50: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
50: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
50: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
50: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
50: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
50: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
50: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
50: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
50: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
50: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
50: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
50: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
50: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
50: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
50: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
50: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
50: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
50: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
50: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
50: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
50: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
50: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
50: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
50: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
50: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
50: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
50: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
50: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
50: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
50: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
50: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
50: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
50: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
50: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
50: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
50: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
50: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
50: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
50: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
50: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
50: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
50: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
50: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
50: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
50: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
50: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
50: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
50: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
50: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
50: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
50: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
50: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
50: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
50: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
50: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
50: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
50: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
50: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
50: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
50: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
50: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
50: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
50: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
50: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
50: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
50: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
50: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
50: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
50: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
50: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
50: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
50: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
50: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
50: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
50: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
50: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
50: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
50: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
50: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
50: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
50: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
50: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
50: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
50: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
50: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
50: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
50: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
50: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
50: v (156x3):
50: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
50: Group statistics
50: T-Coupling : 156 (total 156 atoms)
50: Energy Mon. : 156 (total 156 atoms)
50: Acceleration: 156 (total 156 atoms)
50: Freeze : 156 (total 156 atoms)
50: User1 : 156 (total 156 atoms)
50: User2 : 156 (total 156 atoms)
50: VCM : 156 (total 156 atoms)
50: Compressed X: 156 (total 156 atoms)
50: Or. Res. Fit: 156 (total 156 atoms)
50: QMMM : 156 (total 156 atoms)
50: [ OK ] DumpTest.WorksWithTpr (35 ms)
50: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
50: [ OK ] DumpTest.WorksWithTprAndMdpWriting (4 ms)
50: [----------] 2 tests from DumpTest (40 ms total)
50:
50: [----------] 3 tests from HelpwritingTest
50: [ RUN ] HelpwritingTest.ConvertTprWritesHelp
50: [ OK ] HelpwritingTest.ConvertTprWritesHelp (1 ms)
50: [ RUN ] HelpwritingTest.DumpWritesHelp
50: [ OK ] HelpwritingTest.DumpWritesHelp (1 ms)
50: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp
50: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (1 ms)
50: [----------] 3 tests from HelpwritingTest (3 ms total)
50:
50: [----------] 4 tests from ReportMethodsTest
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: For a correct single-point energy evaluation with nsteps = 0, use
50: continuation = yes to avoid constraining the input coordinates.
50:
50: Generating 1-4 interactions: fudge = 0.5
50:
50: NOTE 2 [file lysozyme.top, line 1465]:
50: System has non-zero total charge: 2.000000
50: Total charge should normally be an integer. See
50: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
50: for discussion on how close it should be to an integer.
50:
50:
50:
50: Number of degrees of freedom in T-Coupling group rest is 465.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: NVE simulation with an initial temperature of zero: will use a Verlet
50: buffer of 10%. Check your energy drift!
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Setting the LD random seed to -155189324
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50:
50: Generated 330891 of the 330891 1-4 parameter combinations
50:
50: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
50: Analysing residue names:
50: There are: 10 Protein residues
50: Analysing Protein...
50:
50: This run will generate roughly 0 Mb of data
50: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
50: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
50: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
50: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
50: [ RUN ] ReportMethodsTest.WritesCorrectInformation
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
50: [ OK ] ReportMethodsTest.WritesCorrectInformation (2 ms)
50: [ RUN ] ReportMethodsTest.ToolEndToEndTest
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
50: section: Methods
50: subsection: Simulation system
50: A system of 1 molecules (156 atoms) was simulated.
50:
50: subsection: Simulation settings
50: A total of 0 ns were simulated with a time step of 1 fs.
50: Neighbor searching was performed every 10 steps.
50: The Cut-off algorithm was used for electrostatic interactions.
50: with a cut-off of 1 nm.
50: A single cut-off of 1.1 nm was used for Van der Waals interactions.
50: [ OK ] ReportMethodsTest.ToolEndToEndTest (2 ms)
50: [----------] 4 tests from ReportMethodsTest (4 ms total)
50:
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: trr version: GMX_trn_file (single precision)
50:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (8 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (7 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (7 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from gro file '', 6 atoms.
50:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (7 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
50: -> frame 0 time 0.000
't= 0.00000', 6 atoms
50:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (7 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
50: Will write tng: Trajectory file (tng format)
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (7 ms)
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (43 ms total)
50:
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from gro file '', 6 atoms.
50:
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
50: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
50: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
50: -> frame 0 time 0.000
't= 0.00000', 6 atoms
50:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (2 ms)
50: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
50: Will write trr: Trajectory in portable xdr format
50: Group 0 ( System) has 6 elements
50: Group 1 (FirstWaterMolecule) has 3 elements
50: Group 2 (SecondWaterMolecule) has 3 elements
50: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
50:
50: Note that major changes are planned in future for trjconv, to improve usability and utility.
50: Select group for output
50: Selected 2: 'SecondWaterMolecule'
50: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (2 ms)
50: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (13 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 21 tests from 5 test cases ran. (5438 ms total)
50: [ PASSED ] 21 tests.
50/65 Test #50: ToolUnitTests ......................... Passed 5.48 sec
test 51
Start 51: FileIOTests
51: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FileIOTests.xml"
51: Test timeout computed to be: 30
51: [==========] Running 42 tests from 10 test cases.
51: [----------] Global test environment set-up.
51: [----------] 4 tests from Checkpoint
51: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent
51: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (1 ms)
51: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent
51: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms)
51: [ RUN ] Checkpoint.KvtRoundTripInt64
51: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms)
51: [ RUN ] Checkpoint.KvtRoundTripReal
51: [ OK ] Checkpoint.KvtRoundTripReal (0 ms)
51: [----------] 4 tests from Checkpoint (1 ms total)
51:
51: [----------] 2 tests from FileMD5Test
51: [ RUN ] FileMD5Test.CanComputeMD5
51: [ OK ] FileMD5Test.CanComputeMD5 (4 ms)
51: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
51: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
51: [----------] 2 tests from FileMD5Test (5 ms total)
51:
51: [----------] 3 tests from MrcSerializer
51: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
51: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
51: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
51: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms)
51: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
51: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (3 ms)
51: [----------] 3 tests from MrcSerializer (3 ms total)
51:
51: [----------] 4 tests from MrcDensityMap
51: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
51: [ OK ] MrcDensityMap.RoundTripIsIdempotent (2 ms)
51: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
51: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms)
51: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
51: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms)
51: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
51: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (3 ms)
51: [----------] 4 tests from MrcDensityMap (7 ms total)
51:
51: [----------] 8 tests from MrcDensityMapHeaderTest
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
51: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
51: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
51: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
51: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
51: [ RUN ] MrcDensityMapHeaderTest.IsSane
51: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
51: [----------] 8 tests from MrcDensityMapHeaderTest (1 ms total)
51:
51: [----------] 10 tests from ReadTest
51: [ RUN ] ReadTest.get_eint_ReadsInteger
51: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side '0.8' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
51: [ RUN ] ReadTest.get_eint_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.get_eint64_ReadsInteger
51: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side '0.8' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
51: [ RUN ] ReadTest.get_eint64_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not an
51: integer value
51:
51:
51: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.get_ereal_ReadsInteger
51: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
51: [ RUN ] ReadTest.get_ereal_ReadsFloat
51: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
51: [ RUN ] ReadTest.get_ereal_WarnsAboutString
51:
51: ERROR 1 [file unknown, line 0]:
51: Right hand side 'hello' for parameter 'test' in parameter file is not a
51: real value
51:
51:
51: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
51: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString
51: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms)
51: [----------] 10 tests from ReadTest (2 ms total)
51:
51: [----------] 1 test from FileIOXdrSerializerTest
51: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
51: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms)
51: [----------] 1 test from FileIOXdrSerializerTest (0 ms total)
51:
51: [----------] 2 tests from TngTest
51: [ RUN ] TngTest.CanOpenTngFile
51: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
51: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
51: [ OK ] TngTest.CanOpenTngFile (0 ms)
51: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
51: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
51: [----------] 2 tests from TngTest (0 ms total)
51:
51: [----------] 4 tests from XvgioTest
51: [ RUN ] XvgioTest.readXvgIntWorks
51: [ OK ] XvgioTest.readXvgIntWorks (1 ms)
51: [ RUN ] XvgioTest.readXvgRealWorks
51: [ OK ] XvgioTest.readXvgRealWorks (1 ms)
51: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks
51: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms)
51: [ RUN ] XvgioTest.readXvgDeprecatedWorks
51: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms)
51: [----------] 4 tests from XvgioTest (3 ms total)
51:
51: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (2 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (4 ms)
51: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
51: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms)
51: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (10 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 42 tests from 10 test cases ran. (34 ms total)
51: [ PASSED ] 42 tests.
51/65 Test #51: FileIOTests ........................... Passed 0.07 sec
test 52
Start 52: SelectionUnitTests
52: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml"
52: Test timeout computed to be: 30
52: [==========] Running 192 tests from 11 test cases.
52: [----------] Global test environment set-up.
52: [----------] 1 test from IndexGroupTest
52: [ RUN ] IndexGroupTest.RemovesDuplicates
52: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
52: [----------] 1 test from IndexGroupTest (0 ms total)
52:
52: [----------] 15 tests from IndexBlockTest
52: [ RUN ] IndexBlockTest.CreatesUnknownBlock
52: [ OK ] IndexBlockTest.CreatesUnknownBlock (1 ms)
52: [ RUN ] IndexBlockTest.CreatesAtomBlock
52: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms)
52: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
52: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms)
52: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
52: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (1 ms)
52: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
52: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms)
52: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
52: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms)
52: [ RUN ] IndexBlockTest.CreatesSingleBlock
52: [ OK ] IndexBlockTest.CreatesSingleBlock (1 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
52: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
52: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
52: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
52: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
52: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
52: [----------] 15 tests from IndexBlockTest (6 ms total)
52:
52: [----------] 11 tests from IndexMapTest
52: [ RUN ] IndexMapTest.InitializesAtomBlock
52: [ OK ] IndexMapTest.InitializesAtomBlock (1 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
52: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
52: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
52: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
52: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms)
52: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
52: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms)
52: [ RUN ] IndexMapTest.InitializesMoleculeBlock
52: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms)
52: [ RUN ] IndexMapTest.MapsSingleBlock
52: [ OK ] IndexMapTest.MapsSingleBlock (0 ms)
52: [ RUN ] IndexMapTest.MapsResidueBlocks
52: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms)
52: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
52: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms)
52: [ RUN ] IndexMapTest.HandlesMultipleRequests
52: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms)
52: [----------] 11 tests from IndexMapTest (7 ms total)
52:
52: [----------] 3 tests from IndexGroupsAndNamesTest
52: [ RUN ] IndexGroupsAndNamesTest.containsNames
52: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
52: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
52: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms)
52: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
52: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms)
52: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total)
52:
52: [----------] 15 tests from NeighborhoodSearchTest
52: [ RUN ] NeighborhoodSearchTest.SimpleSearch
52: [ OK ] NeighborhoodSearchTest.SimpleSearch (39 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
52: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (43 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchBox
52: [ OK ] NeighborhoodSearchTest.GridSearchBox (7 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
52: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (23 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
52: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (13 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
52: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (5 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
52: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (7 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
52: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
52: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (110 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
52: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
52: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
52: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
52: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
52: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
52: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
52: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (9 ms)
52: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
52: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (2 ms)
52: [----------] 15 tests from NeighborhoodSearchTest (261 ms total)
52:
52: [----------] 12 tests from PositionCalculationTest
52: [ RUN ] PositionCalculationTest.ComputesAtomPositions
52: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
52: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
52: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
52: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
52: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
52: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
52: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms)
52: [ RUN ] PositionCalculationTest.ComputesPositionMask
52: [ OK ] PositionCalculationTest.ComputesPositionMask (1 ms)
52: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
52: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms)
52: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
52: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms)
52: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
52: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms)
52: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
52: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms)
52: [----------] 12 tests from PositionCalculationTest (9 ms total)
52:
52: [----------] 29 tests from SelectionCollectionTest
52: [ RUN ] SelectionCollectionTest.HandlesNoSelections
52: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms)
52: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
52: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
52: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
52: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms)
52: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
52: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
52: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
52: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
52: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
52: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
52: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
52: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
52: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
52: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
52: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
52: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
52: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
52: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms)
52: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
52: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (2 ms)
52: [----------] 29 tests from SelectionCollectionTest (33 ms total)
52:
52: [----------] 14 tests from SelectionCollectionInteractiveTest
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
52: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
52: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
52: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
52: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
52: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
52: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (2 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
52: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
52: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (1 ms)
52: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
52: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms)
52: [----------] 14 tests from SelectionCollectionInteractiveTest (20 ms total)
52:
52: [----------] 66 tests from SelectionCollectionDataTest
52: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
52: [ OK ] SelectionCollectionDataTest.HandlesAllNone (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
52: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResnr
52: [ OK ] SelectionCollectionDataTest.HandlesResnr (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
52: [ OK ] SelectionCollectionDataTest.HandlesResIndex (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
52: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
52: [ OK ] SelectionCollectionDataTest.HandlesAtomname (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
52: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
52: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesChain
52: [ OK ] SelectionCollectionDataTest.HandlesChain (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMass
52: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesCharge
52: [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
52: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
52: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
52: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBeta
52: [ OK ] SelectionCollectionDataTest.HandlesBeta (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesResname
52: [ OK ] SelectionCollectionDataTest.HandlesResname (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
52: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
52: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
52: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (12 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (5 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
52: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (5 ms)
52: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
52: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (3 ms)
52: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
52: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
52: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
52: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
52: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
52: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
52: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
52: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
52: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
52: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
52: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
52: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
52: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
52: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
52: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
52: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
52: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
52: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
52: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
52: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
52: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
52: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
52: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
52: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (4 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
52: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
52: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
52: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
52: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
52: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
52: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (3 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
52: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
52: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (2 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (1 ms)
52: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
52: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms)
52: [----------] 66 tests from SelectionCollectionDataTest (159 ms total)
52:
52: [----------] 17 tests from SelectionOptionTest
52: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
52: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
52: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
52: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (1 ms)
52: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
52: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (1 ms)
52: [ RUN ] SelectionOptionTest.ChecksEmptySelections
52: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
52: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
52: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooManySelections
52: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
52: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
52: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesAdjuster
52: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
52: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
52: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
52: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
52: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
52: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms)
52: [----------] 17 tests from SelectionOptionTest (15 ms total)
52:
52: [----------] 9 tests from SelectionFileOptionTest
52: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
52: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
52: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
52: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
52: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
52: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
52: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
52: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
52: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
52: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms)
52: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
52: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms)
52: [----------] 9 tests from SelectionFileOptionTest (8 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 192 tests from 11 test cases ran. (522 ms total)
52: [ PASSED ] 192 tests.
52/65 Test #52: SelectionUnitTests .................... Passed 0.56 sec
test 53
Start 53: MdrunOutputTests
53: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml"
53: Test timeout computed to be: 600
53: [==========] Running 12 tests from 5 test cases.
53: [----------] Global test environment set-up.
53: [----------] 1 test from MdrunTest
53: [ RUN ] MdrunTest.WritesHelp
53: No protocol specified
53: [ OK ] MdrunTest.WritesHelp (30 ms)
53: [----------] 1 test from MdrunTest (31 ms total)
53:
53: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
53: No protocol specified
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -1217544257
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.436 0.218 199.9
53: (ns/day) (hour/ns)
53: Performance: 0.792 30.301
53:
Reading frame 0 time 0.000
53: # Atoms 6
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (241 ms)
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -1918961282
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.307 0.154 199.8
53: (ns/day) (hour/ns)
53: Performance: 1.123 21.372
53:
Reading frame 0 time 0.000
53: # Atoms 6
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (174 ms)
53: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
53: Generating 1-4 interactions: fudge = 0.5
53: Number of degrees of freedom in T-Coupling group rest is 9.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
53: NVE simulation: will use the initial temperature of 2573.591 K for
53: determining the Verlet buffer size
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc2'
53: 1 steps, 0.0 ps.
53: Setting the LD random seed to -707026961
53:
53: Generated 3 of the 3 non-bonded parameter combinations
53:
53: Generated 3 of the 3 1-4 parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.375 0.188 199.8
53: (ns/day) (hour/ns)
53: Performance: 0.922 26.043
53:
Reading frame 0 time 0.000
53: # Atoms 3
53:
Reading frame 1 time 0.001
Last frame 1 time 0.001
53:
53:
53: Item #frames Timestep (ps)
53: Step 2 0.001
53: Time 2 0.001
53: Lambda 0
53: Coords 2 0.001
53: Velocities 0
53: Forces 0
53: Box 2 0.001
53: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
53: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (208 ms)
53: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (623 ms total)
53:
53: [----------] 2 tests from Argon12/OutputFiles
53: No protocol specified
53: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
53: that with the Verlet scheme, nstlist has no effect on the accuracy of
53: your simulation.
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: Setting nstcalcenergy (100) equal to nstenergy (4)
53:
53: Number of degrees of freedom in T-Coupling group System is 33.00
53:
53: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
53: NVE simulation: will use the initial temperature of 68.810 K for
53: determining the Verlet buffer size
53:
53:
53: There were 3 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'Argon'
53: 16 steps, 0.0 ps.
53: Generated 1 of the 1 non-bonded parameter combinations
53:
53: Excluding 1 bonded neighbours molecule type 'Argon'
53:
53: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
53:
53: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.396 0.198 199.9
53: (ns/day) (hour/ns)
53: Performance: 7.404 3.242
53: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (217 ms)
53: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
53: that with the Verlet scheme, nstlist has no effect on the accuracy of
53: your simulation.
53:
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: Setting nstcalcenergy (100) equal to nstenergy (4)
53:
53: Number of degrees of freedom in T-Coupling group System is 33.00
53:
53: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
53: NVE simulation: will use the initial temperature of 68.810 K for
53: determining the Verlet buffer size
53:
53:
53: There were 3 notes
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
53: Can not increase nstlist because an NVE ensemble is used
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'Argon'
53: 16 steps, 0.0 ps.
53: Generated 1 of the 1 non-bonded parameter combinations
53:
53: Excluding 1 bonded neighbours molecule type 'Argon'
53:
53: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
53:
53: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.394 0.197 199.9
53: (ns/day) (hour/ns)
53: Performance: 7.446 3.223
53: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (217 ms)
53: [----------] 2 tests from Argon12/OutputFiles (434 ms total)
53:
53: [----------] 3 tests from MdrunCanWrite/Trajectories
53: No protocol specified
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to 1848639103
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.496 0.248 199.9
53: (ns/day) (hour/ns)
53: Performance: 2.436 9.854
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (270 ms)
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to -33890887
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.323 0.162 199.8
53: (ns/day) (hour/ns)
53: Performance: 3.743 6.411
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (183 ms)
53: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 6 steps, 0.0 ps.
53: Setting the LD random seed to -537857027
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.421 0.211 199.8
53: (ns/day) (hour/ns)
53: Performance: 2.867 8.370
53: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (233 ms)
53: [----------] 3 tests from MdrunCanWrite/Trajectories (686 ms total)
53:
53: [----------] 3 tests from MdrunCanWrite/NptTrajectories
53: No protocol specified
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to -1109655553
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.308 0.154 199.7
53: (ns/day) (hour/ns)
53: Performance: 1.678 14.301
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (179 ms)
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to -269624836
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.320 0.160 199.7
53: (ns/day) (hour/ns)
53: Performance: 1.616 14.848
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (190 ms)
53: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
53: Number of degrees of freedom in T-Coupling group System is 12.00
53:
53: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There was 1 note
53: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
53: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
53: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
53:
53: Using 1 MPI thread
53: Using 2 OpenMP threads
53:
53:
53: NOTE: The number of threads is not equal to the number of (logical) cores
53: and the -pin option is set to auto: will not pin threads to cores.
53: This can lead to significant performance degradation.
53: Consider using -pin on (and -pinoffset in case you run multiple jobs).
53:
53: WARNING: Using the slow plain C kernels. This should
53: not happen during routine usage on supported platforms.
53: starting mdrun 'spc-and-methanol'
53: 2 steps, 0.0 ps.
53: Setting the LD random seed to -912277585
53:
53: Generated 8 of the 10 non-bonded parameter combinations
53:
53: Excluding 2 bonded neighbours molecule type 'Methanol'
53:
53: Excluding 2 bonded neighbours molecule type 'SOL'
53:
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53:
53: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
53:
53: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
53:
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53:
53: This run will generate roughly 0 Mb of data
53:
53: Writing final coordinates.
53:
53: Core t (s) Wall t (s) (%)
53: Time: 0.467 0.234 199.8
53: (ns/day) (hour/ns)
53: Performance: 1.110 21.625
53: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (263 ms)
53: [----------] 3 tests from MdrunCanWrite/NptTrajectories (634 ms total)
53:
53: [----------] Global test environment tear-down
53: [==========] 12 tests from 5 test cases ran. (2494 ms total)
53: [ PASSED ] 12 tests.
53/65 Test #53: MdrunOutputTests ...................... Passed 2.53 sec
test 54
Start 54: MdrunModulesTests
54: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml"
54: Test timeout computed to be: 600
54: [==========] Running 15 tests from 3 test cases.
54: [----------] Global test environment set-up.
54: [----------] 9 tests from DensityFittingTest
54: No protocol specified
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -3.85654101644806e+03
54: Maximum force = 2.88468568366558e+03 on atom 3
54: Norm of force = 1.07544474716821e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to 914030351
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (36 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -9.82084736967821e+03
54: Maximum force = 4.73310933913648e+03 on atom 2
54: Norm of force = 1.78012183879532e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to 2029780845
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (27 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (19 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -9.76043429797377e+03
54: Maximum force = 4.63447892024619e+03 on atom 2
54: Norm of force = 1.75756003355952e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to 2008727189
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (23 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (17 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -3.85654101644806e+03
54: Maximum force = 2.88468568366558e+03 on atom 3
54: Norm of force = 1.07544474716821e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to 1700198369
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (22 ms)
54: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = -2.71386626596691e+04
54: Maximum force = 4.34097106676756e+03 on atom 2
54: Norm of force = 1.25497916295893e+03
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 Setting the LD random seed to -4194309
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (23 ms)
54: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
54:
54: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1050:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out.
54: Setting the LD random seed to -1241620617
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (22 ms)
54: [ RUN ] DensityFittingTest.CheckpointWorks
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
54: Setting nstcalcenergy (100) equal to nstenergy (2)
54:
54: Number of degrees of freedom in T-Coupling group rest is 33.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
54: NVE simulation: will use the initial temperature of 68.810 K for
54: determining the Verlet buffer size
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting mdrun 'Argon'
54: 2 steps, 0.0 ps.
54: Setting the LD random seed to -4194321
54:
54: Generated 1 of the 1 non-bonded parameter combinations
54:
54: Excluding 1 bonded neighbours molecule type 'Argon'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.383 0.192 199.9
54: (ns/day) (hour/ns)
54: Performance: 1.353 17.737
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
54: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
54: Can not increase nstlist because an NVE ensemble is used
54:
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting mdrun 'Argon'
54: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.247 0.124 199.8
54: (ns/day) (hour/ns)
54: Performance: 3.489 6.878
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (354 ms)
54: [----------] 9 tests from DensityFittingTest (550 ms total)
54:
54: [----------] 4 tests from MimicTest
54: No protocol specified
54: [ RUN ] MimicTest.OneQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.002 0.001 190.3
54: (ns/day) (hour/ns)
54: Performance: 71.140 0.337
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 508413433
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.OneQuantumMol (23 ms)
54: [ RUN ] MimicTest.AllQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.002 0.001 190.1
54: (ns/day) (hour/ns)
54: Performance: 73.927 0.325
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1342178433
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.AllQuantumMol (24 ms)
54: [ RUN ] MimicTest.TwoQuantumMol
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 21.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: NVE simulation with an initial temperature of zero: will use a Verlet
54: buffer of 10%. Check your energy drift!
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
54:
54: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.002 0.001 189.3
54: (ns/day) (hour/ns)
54: Performance: 72.218 0.332
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -876801
54:
54: Generated 10 of the 10 non-bonded parameter combinations
54:
54: Generated 10 of the 10 1-4 parameter combinations
54:
54: Excluding 2 bonded neighbours molecule type 'SOL'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.TwoQuantumMol (22 ms)
54: [ RUN ] MimicTest.BondCuts
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: For a correct single-point energy evaluation with nsteps = 0, use
54: continuation = yes to avoid constraining the input coordinates.
54:
54: Generating 1-4 interactions: fudge = 0.5
54: Number of degrees of freedom in T-Coupling group rest is 66.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: NVE simulation: will use the initial temperature of 300.368 K for
54: determining the Verlet buffer size
54:
54:
54: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 3 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
54: Can not increase nstlist because an NVE ensemble is used
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
54:
54: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
54:
Reading frame 0 time 0.000
Last frame 0 time 0.000
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.004 0.002 194.8
54: (ns/day) (hour/ns)
54: Performance: 38.054 0.631
54: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
54:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -587795969
54:
54: Generated 2211 of the 2211 non-bonded parameter combinations
54:
54: Generated 2211 of the 2211 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] MimicTest.BondCuts (74 ms)
54: [----------] 4 tests from MimicTest (148 ms total)
54:
54: [----------] 2 tests from WithIntegrator/ImdTest
54: No protocol specified
54: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
54: Generating 1-4 interactions: fudge = 1
54:
54: NOTE 1 [file glycine_vacuo.top, line 12]:
54: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
54: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
54: Number of degrees of freedom in T-Coupling group System is 27.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
54: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
54:
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: IMD: Enabled. This simulation will accept incoming IMD connections.
54: IMD: Pulling from IMD remote is enabled (-imdpull).
54: IMD: Setting port for connection requests to 0.
54: IMD: Setting up incoming socket.
54: IMD: Listening for IMD connection on port 48523.
54: IMD: -imdwait not set, starting simulation.
54: starting mdrun 'Glycine'
54: 2 steps, 0.0 ps.
54: Setting the LD random seed to -8337
54:
54: Generated 20503 of the 20503 non-bonded parameter combinations
54:
54: Generated 17396 of the 20503 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Glycine'
54:
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
54:
54: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
54:
54: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
54:
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54:
54: This run will generate roughly 0 Mb of data
54:
54: Writing final coordinates.
54:
54: Core t (s) Wall t (s) (%)
54: Time: 0.367 0.184 199.8
54: (ns/day) (hour/ns)
54: Performance: 2.823 8.502
54: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (654 ms)
54: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
54:
54: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
54: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
54: apply to steep.
54:
54: Generating 1-4 interactions: fudge = 1
54: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
54: Number of degrees of freedom in T-Coupling group System is 27.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
54: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
54: Using 1 MPI thread
54: Using 2 OpenMP threads
54:
54:
54: NOTE: The number of threads is not equal to the number of (logical) cores
54: and the -pin option is set to auto: will not pin threads to cores.
54: This can lead to significant performance degradation.
54: Consider using -pin on (and -pinoffset in case you run multiple jobs).
54:
54: WARNING: Using the slow plain C kernels. This should
54: not happen during routine usage on supported platforms.
54:
54: IMD: Enabled. This simulation will accept incoming IMD connections.
54: IMD: Pulling from IMD remote is enabled (-imdpull).
54: IMD: Setting port for connection requests to 0.
54: IMD: Setting up incoming socket.
54: IMD: Listening for IMD connection on port 53973.
54: IMD: -imdwait not set, starting simulation.
54:
54: Steepest Descents:
54: Tolerance (Fmax) = 1.00000e+01
54: Number of steps = 2
54:
54: Energy minimization reached the maximum number of steps before the forces
54: reached the requested precision Fmax < 10.
54:
54: writing lowest energy coordinates.
54:
54: Steepest Descents did not converge to Fmax < 10 in 3 steps.
54: Potential Energy = 1.19770464690297e+03
54: Maximum force = 1.77948604657896e+04 on atom 9
54: Norm of force = 7.87328617833980e+03
54: Setting the LD random seed to 1006628838
54:
54: Generated 20503 of the 20503 non-bonded parameter combinations
54:
54: Generated 17396 of the 20503 1-4 parameter combinations
54:
54: Excluding 3 bonded neighbours molecule type 'Glycine'
54:
54: This run will generate roughly 0 Mb of data
54: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (463 ms)
54: [----------] 2 tests from WithIntegrator/ImdTest (1118 ms total)
54:
54: [----------] Global test environment tear-down
54: [==========] 15 tests from 3 test cases ran. (1881 ms total)
54: [ PASSED ] 15 tests.
54/65 Test #54: MdrunModulesTests ..................... Passed 1.91 sec
test 55
Start 55: MdrunIOTests
55: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunIOTests.xml"
55: Test timeout computed to be: 600
55: [==========] Running 61 tests from 10 test cases.
55: [----------] Global test environment set-up.
55: [----------] 3 tests from GromppTest
55: No protocol specified
55: [ RUN ] GromppTest.EmptyMdpFileWorks
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Number of degrees of freedom in T-Coupling group rest is 12.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -22024453
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.EmptyMdpFileWorks (13 ms)
55: [ RUN ] GromppTest.SimulatedAnnealingWorks
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Simulated annealing for group rest: Periodic, 4 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 2.0 320.0
55: 4.0 320.0
55: 6.0 298.0
55: Number of degrees of freedom in T-Coupling group rest is 12.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -136086529
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.SimulatedAnnealingWorks (12 ms)
55: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: For a correct single-point energy evaluation with nsteps = 0, use
55: continuation = yes to avoid constraining the input coordinates.
55:
55: Simulated annealing for group Methanol: Single, 3 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 3.0 280.0
55: 6.0- 270.0
55: Simulated annealing for group SOL: Periodic, 4 timepoints
55: Time (ps) Temperature (K)
55: 0.0 298.0
55: 2.0 320.0
55: 4.0 320.0
55: 6.0 298.0
55: Number of degrees of freedom in T-Coupling group Methanol is 7.20
55: Number of degrees of freedom in T-Coupling group SOL is 4.80
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: NVE simulation: will use the initial temperature of 1046.791 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Setting the LD random seed to -738213897
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (12 ms)
55: [----------] 3 tests from GromppTest (38 ms total)
55:
55: [----------] 6 tests from MdrunTerminationTest
55: No protocol specified
55: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -9970725
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.404 0.202 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.281 18.738
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.306 0.153 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.694 14.171
55: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (389 ms)
55: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 1, rlist from 1.024 to 1
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 100 steps, 0.1 ps.
55:
55: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
55: Setting the LD random seed to -562122785
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.292 0.146 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.773 13.539
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Setting nsteps to 102
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 100
55: Runtime for the run 0.1 ps
55: Run end step 100
55: Run end time 0.1 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 102
55: Runtime for the run 0.102 ps
55: Run end step 102
55: Run end time 0.102 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.290 0.145 199.8
55: (ns/day) (hour/ns)
55: Performance: 60.144 0.399
55: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (324 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -402784397
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.294 0.147 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.762 13.622
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.514 0.257 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.009 23.797
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Setting nsteps to 6
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 6
55: Runtime for the run 0.006 ps
55: Run end step 6
55: Run end time 0.006 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.311 0.156 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.664 14.420
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Setting nsteps to 8
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 6
55: Runtime for the run 0.006 ps
55: Run end step 6
55: Run end time 0.006 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 8
55: Runtime for the run 0.008 ps
55: Run end step 8
55: Run end time 0.008 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.314 0.157 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.648 14.566
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.001 0.000 164.9
55: (ns/day) (hour/ns)
55: Performance: 200.769 0.120
55: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (773 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to 1064564731
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.309 0.154 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.679 14.296
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps.
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.282 0.141 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.064 7.833
55: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (323 ms)
55: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -1435501105
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.326 0.163 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.590 15.095
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Setting nsteps to 4
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (184 ms)
55: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There was 1 note
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 2 steps, 0.0 ps.
55: Setting the LD random seed to -542253153
55:
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.306 0.153 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.694 14.169
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Setting nsteps to 4
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
55: Input file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 2
55: Runtime for the run 0.002 ps
55: Run end step 2
55: Run end time 0.002 ps
55:
55:
55: Output file:
55: Run start step 0
55: Run start time 0 ps
55: Step to be made during run 4
55: Runtime for the run 0.004 ps
55: Run end step 4
55: Run end time 0.004 ps
55:
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.497 0.249 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.042 23.031
55: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (430 ms)
55: [----------] 6 tests from MdrunTerminationTest (2424 ms total)
55:
55: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks
55: No protocol specified
55: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.369 0.185 199.8
55: (ns/day) (hour/ns)
55: Performance: 7.951 3.018
55: trr version: GMX_trn_file (double precision)
55:
55:
55: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (204 ms)
55: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.374 0.187 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.842 3.060
55:
55:
55: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (208 ms)
55: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (412 ms total)
55:
55: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
55: No protocol specified
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.410 0.205 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.155 3.354
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.552 0.276 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.816 8.524
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.401 0.201 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.878 6.189
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (728 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.401 0.200 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.332 3.273
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.436 0.218 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.565 6.732
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.483 0.242 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.219 7.455
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (706 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.566 0.283 199.9
55: (ns/day) (hour/ns)
55: Performance: 5.187 4.627
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.423 0.212 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.674 6.532
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.417 0.209 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.725 6.442
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (747 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.385 0.193 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.630 3.146
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.385 0.193 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.032 5.952
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.583 0.291 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.668 8.994
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (721 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.401 0.201 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.323 3.277
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.352 0.176 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.415 5.436
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.372 0.186 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.181 5.741
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (600 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 2573.591 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.415 0.208 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.073 3.393
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.502 0.251 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.100 7.742
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.388 0.194 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.005 5.993
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (698 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.376 0.188 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.814 3.072
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.372 0.186 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.174 5.750
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.333 0.167 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.660 5.150
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (581 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 9.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps.
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 3 of the 3 non-bonded parameter combinations
55:
55: Generated 3 of the 3 1-4 parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.613 0.307 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.790 5.011
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.385 0.192 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.040 5.941
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc2'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.416 0.208 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.738 6.420
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (756 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.363 0.182 199.8
55: (ns/day) (hour/ns)
55: Performance: 8.085 2.968
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.485 0.243 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.204 7.491
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.431 0.216 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.605 6.657
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (798 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: NVE simulation: will use the initial temperature of 456.887 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 6 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.611 0.306 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.801 4.999
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.366 0.183 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.245 5.654
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.444 0.222 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.498 6.862
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (864 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.605 0.303 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.853 4.945
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.367 0.184 199.6
55: (ns/day) (hour/ns)
55: Performance: 4.233 5.670
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.407 0.204 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.816 6.289
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (913 ms)
55: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55:
55: NOTE 3 [file unknown]:
55: You are using constraints on all bonds, whereas the forcefield has been
55: parametrized only with constraints involving hydrogen atoms. We suggest
55: using constraints = h-bonds instead, this will also improve performance.
55:
55: Number of degrees of freedom in T-Coupling group System is 23.00
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: There are 9 non-linear virtual site constructions. Their contribution to
55: the energy error is approximated. In most cases this does not affect the
55: error significantly.
55:
55:
55: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 5 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps.
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2145 of the 2145 non-bonded parameter combinations
55:
55: Generated 2145 of the 2145 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
55:
55: turning all bonds into constraints...
55:
55: Cleaning up constraints and constant bonded interactions with virtual sites
55:
55: Removed 18 Angles with virtual sites, 21 left
55:
55: Removed 10 Proper Dih.s with virtual sites, 44 left
55:
55: Converted 15 Constraints with virtual sites to connections, 7 left
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.553 0.277 199.9
55: (ns/day) (hour/ns)
55: Performance: 5.308 4.522
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.398 0.199 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.900 6.154
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Alanine dipeptide in vacuo'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.416 0.208 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.736 6.425
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (884 ms)
55: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (9000 ms total)
55:
55: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
55: No protocol specified
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.462 0.231 199.8
55: (ns/day) (hour/ns)
55: Performance: 6.353 3.778
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.468 0.234 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.319 7.230
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.476 0.238 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.266 7.348
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (834 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 293.480 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 4 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.479 0.239 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.136 3.911
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.686 0.343 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.267 10.586
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.531 0.266 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.926 8.202
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (965 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.585 0.293 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.014 4.787
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.461 0.231 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.368 7.125
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.492 0.246 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.157 7.602
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1004 ms)
55: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Generating 1-4 interactions: fudge = 0.5
55: Number of degrees of freedom in T-Coupling group System is 79.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps.
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 2485 of the 2485 non-bonded parameter combinations
55:
55: Generated 2485 of the 2485 1-4 parameter combinations
55:
55: Excluding 3 bonded neighbours molecule type 'nonanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.555 0.278 199.8
55: (ns/day) (hour/ns)
55: Performance: 5.289 4.538
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.467 0.234 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.329 7.210
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun '30 system in water'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.502 0.251 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.096 7.751
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (946 ms)
55: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (3749 ms total)
55:
55: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
55: No protocol specified
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.346 0.173 199.8
55: (ns/day) (hour/ns)
55: Performance: 8.484 2.829
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.554 0.277 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.804 8.559
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.419 0.209 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.714 6.462
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (698 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.433 0.217 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.776 3.542
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.341 0.171 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.552 5.273
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.638 0.319 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.438 9.842
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (740 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.407 0.204 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.205 3.331
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.405 0.203 199.6
55: (ns/day) (hour/ns)
55: Performance: 3.835 6.258
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.551 0.276 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.822 8.506
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (714 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.423 0.212 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.936 3.460
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.674 0.337 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.306 10.408
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.467 0.234 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.328 7.212
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (815 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.422 0.211 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.967 3.445
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.406 0.203 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.829 6.268
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.401 0.200 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.880 6.185
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (648 ms)
55: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.402 0.201 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.301 3.287
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.406 0.203 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.829 6.267
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.453 0.227 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.429 6.999
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (664 ms)
55: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (4280 ms total)
55:
55: [----------] 6 tests from NPH/MdrunNoAppendContinuationIsExact
55: No protocol specified
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.388 0.194 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.567 3.172
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.605 0.303 199.8
55: (ns/day) (hour/ns)
55: Performance: 2.568 9.344
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.454 0.227 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.425 7.007
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (757 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.401 0.201 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.318 3.280
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.406 0.203 199.7
55: (ns/day) (hour/ns)
55: Performance: 3.824 6.276
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.449 0.225 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.463 6.931
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (664 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.435 0.218 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.749 3.556
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.389 0.195 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.991 6.013
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.437 0.219 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.557 6.747
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (665 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.401 0.201 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.316 3.280
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.522 0.261 199.8
55: (ns/day) (hour/ns)
55: Performance: 2.978 8.060
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.453 0.227 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.428 7.002
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (722 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.468 0.234 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.280 3.822
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.356 0.178 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.362 5.502
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.436 0.218 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.565 6.732
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (665 ms)
55: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: NVE simulation: will use the initial temperature of 68.810 K for
55: determining the Verlet buffer size
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.582 0.291 199.9
55: (ns/day) (hour/ns)
55: Performance: 5.043 4.760
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.356 0.178 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.367 5.495
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.420 0.210 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.700 6.487
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (722 ms)
55: [----------] 6 tests from NPH/MdrunNoAppendContinuationIsExact (4197 ms total)
55:
55: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact
55: No protocol specified
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.404 0.202 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.258 3.307
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.389 0.195 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.994 6.008
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.536 0.268 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.900 8.277
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (699 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.402 0.201 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.308 3.284
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.389 0.195 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.994 6.010
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.404 0.202 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.851 6.233
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (632 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.567 0.284 199.9
55: (ns/day) (hour/ns)
55: Performance: 5.179 4.635
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.405 0.203 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.832 6.263
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.420 0.210 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.703 6.480
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (731 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.452 0.226 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.496 3.695
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.372 0.186 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.173 5.752
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.619 0.310 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.510 9.562
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (757 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.400 0.200 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.348 3.266
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.372 0.186 199.7
55: (ns/day) (hour/ns)
55: Performance: 4.172 5.753
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.452 0.226 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.437 6.983
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (647 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.369 0.184 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.967 3.013
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.555 0.278 199.8
55: (ns/day) (hour/ns)
55: Performance: 2.800 8.572
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.587 0.293 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.650 9.056
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (788 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55:
55: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Using Berendsen pressure coupling invalidates the true ensemble for the
55: thermostat
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: There was 1 warning
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55:
55: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
55: Using Berendsen pressure coupling invalidates the true ensemble for the
55: thermostat
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: There was 1 warning
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 2.368 1.184 200.0
55: (ns/day) (hour/ns)
55: Performance: 1.240 19.348
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.444 0.222 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.498 6.860
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.422 0.211 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.682 6.519
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (1669 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.507 0.254 199.9
55: (ns/day) (hour/ns)
55: Performance: 5.786 4.148
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.376 0.188 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.128 5.815
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.385 0.192 199.9
55: (ns/day) (hour/ns)
55: Performance: 4.042 5.937
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (675 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
55: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.395 0.198 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.436 3.227
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.387 0.193 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.019 5.972
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.600 0.300 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.589 9.270
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (731 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.378 0.189 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.768 3.090
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.386 0.193 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.020 5.970
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.418 0.209 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.722 6.448
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (631 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.429 0.214 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.852 3.503
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.586 0.293 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.652 9.050
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.434 0.217 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.584 6.697
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (764 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
55: The Berendsen thermostat does not generate the correct kinetic energy
55: distribution. You might want to consider using the V-rescale thermostat.
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.393 0.197 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.462 3.216
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.370 0.185 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.202 5.712
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.626 0.313 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.482 9.671
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (734 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.547 0.273 199.9
55: (ns/day) (hour/ns)
55: Performance: 5.373 4.467
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.390 0.195 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.985 6.022
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.438 0.219 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.546 6.769
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (726 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.423 0.211 199.9
55: (ns/day) (hour/ns)
55: Performance: 6.949 3.454
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.656 0.328 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.371 10.124
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.439 0.219 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.544 6.773
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (790 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.389 0.195 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.541 3.183
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.556 0.278 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.797 8.580
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.572 0.286 199.9
55: (ns/day) (hour/ns)
55: Performance: 2.716 8.837
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (797 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15
55: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (0 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16
55: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (0 ms)
55: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.406 0.203 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.227 3.321
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.341 0.171 199.8
55: (ns/day) (hour/ns)
55: Performance: 4.559 5.264
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.456 0.228 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.410 7.039
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (631 ms)
55: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (12403 ms total)
55:
55: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
55: No protocol specified
55: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
55: that with the Verlet scheme, nstlist has no effect on the accuracy of
55: your simulation.
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
55: Setting nstcalcenergy (100) equal to nstenergy (4)
55:
55: Number of degrees of freedom in T-Coupling group System is 33.00
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps.
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55: Generated 1 of the 1 non-bonded parameter combinations
55:
55: Excluding 1 bonded neighbours molecule type 'Argon'
55:
55: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
55:
55: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.406 0.203 199.9
55: (ns/day) (hour/ns)
55: Performance: 7.227 3.321
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 8 steps, 0.0 ps.
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.507 0.254 199.8
55: (ns/day) (hour/ns)
55: Performance: 3.064 7.833
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
55:
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'Argon'
55: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.389 0.195 199.9
55: (ns/day) (hour/ns)
55: Performance: 3.994 6.009
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (683 ms)
55: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (683 ms total)
55:
55: [----------] 3 tests from Checking/InitialConstraintsTest
55: No protocol specified
55: [ RUN ] Checking/InitialConstraintsTest.Works/0
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to -3280919
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.306 0.153 199.8
55: (ns/day) (hour/ns)
55: Performance: 1.128 21.276
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (183 ms)
55: [ RUN ] Checking/InitialConstraintsTest.Works/1
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 2 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to 1072756734
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.374 0.187 199.9
55: (ns/day) (hour/ns)
55: Performance: 0.924 25.967
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (200 ms)
55: [ RUN ] Checking/InitialConstraintsTest.Works/2
55:
55: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: Integrator method md-vv-avek is implemented primarily for validation
55: purposes; for molecular dynamics, you should probably be using md or md-vv
55:
55: Number of degrees of freedom in T-Coupling group rest is 11.00
55:
55: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: NVE simulation: will use the initial temperature of 1141.954 K for
55: determining the Verlet buffer size
55:
55:
55: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
55: You are using a plain Coulomb cut-off, which might produce artifacts.
55: You might want to consider using PME electrostatics.
55:
55:
55:
55: There were 3 notes
55: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
55: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
55: Can not increase nstlist because an NVE ensemble is used
55: Using 1 MPI thread
55: Using 2 OpenMP threads
55:
55:
55: NOTE: The number of threads is not equal to the number of (logical) cores
55: and the -pin option is set to auto: will not pin threads to cores.
55: This can lead to significant performance degradation.
55: Consider using -pin on (and -pinoffset in case you run multiple jobs).
55:
55: WARNING: Using the slow plain C kernels. This should
55: not happen during routine usage on supported platforms.
55: starting mdrun 'spc-and-methanol'
55: 1 steps, 0.0 ps.
55: Setting the LD random seed to 1659664111
55:
55: Generated 8 of the 10 non-bonded parameter combinations
55:
55: Excluding 2 bonded neighbours molecule type 'Methanol'
55:
55: turning H bonds into constraints...
55:
55: Excluding 2 bonded neighbours molecule type 'SOL'
55:
55: turning H bonds into constraints...
55:
55: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
55:
55: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
55:
55: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
55:
55: Note that mdrun will redetermine rlist based on the actual pair-list setup
55:
55: This run will generate roughly 0 Mb of data
55:
55: Writing final coordinates.
55:
55: Core t (s) Wall t (s) (%)
55: Time: 0.323 0.162 199.9
55: (ns/day) (hour/ns)
55: Performance: 1.070 22.432
55: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file
55:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (174 ms)
55: [----------] 3 tests from Checking/InitialConstraintsTest (557 ms total)
55:
55: [----------] Global test environment tear-down
55: [==========] 61 tests from 10 test cases ran. (37919 ms total)
55: [ PASSED ] 61 tests.
55/65 Test #55: MdrunIOTests .......................... Passed 37.96 sec
test 56
Start 56: MdrunTests
56: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTests.xml"
56: Test timeout computed to be: 600
56: [==========] Running 14 tests from 6 test cases.
56: [----------] Global test environment set-up.
56: [----------] 1 test from OriresTest
56: No protocol specified
56: [ RUN ] OriresTest.OriresCanRun
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
56: The Berendsen thermostat does not generate the correct kinetic energy
56: distribution. You might want to consider using the V-rescale thermostat.
56:
56: Generating 1-4 interactions: fudge = 0.5
56: Number of degrees of freedom in T-Coupling group System is 518.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
56: You are using a plain Coulomb cut-off, which might produce artifacts.
56: You might want to consider using PME electrostatics.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
56: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
56:
56:
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
56: 10 steps, 0.0 ps.
56: Setting the LD random seed to -558121377
56:
56: Generated 2145 of the 2145 non-bonded parameter combinations
56:
56: Generated 2145 of the 2145 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
56:
56: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
56:
56: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
56:
56: Note that mdrun will redetermine rlist based on the actual pair-list setup
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.342 0.171 199.8
56: (ns/day) (hour/ns)
56: Performance: 11.089 2.164
56: [ OK ] OriresTest.OriresCanRun (706 ms)
56: [----------] 1 test from OriresTest (706 ms total)
56:
56: [----------] 1 test from CompelTest
56: No protocol specified
56: [ RUN ] CompelTest.SwapCanRun
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: The Berendsen thermostat does not generate the correct kinetic energy
56: distribution. You might want to consider using the V-rescale thermostat.
56:
56: Generating 1-4 interactions: fudge = 0.5
56: Split0 group 'Ch0' contains 83 atoms.
56: Split1 group 'Ch1' contains 83 atoms.
56: Solvent group 'SOL' contains 11931 atoms.
56: Swap group 'NA+' contains 19 atoms.
56: Swap group 'CL-' contains 19 atoms.
56: Number of degrees of freedom in T-Coupling group System is 27869.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
56: You are using a plain Coulomb cut-off, which might produce artifacts.
56: You might want to consider using PME electrostatics.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: SWAP: Determining initial numbers of ions per compartment.
56: SWAP: Setting pointers for checkpoint writing
56: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
56: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
56: starting mdrun 'Channel_coco in octane membrane'
56: 2 steps, 0.0 ps.
56: Setting the LD random seed to -480265220
56:
56: Generated 330891 of the 330891 non-bonded parameter combinations
56:
56: Generated 330891 of the 330891 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein'
56:
56: turning all bonds into constraints...
56:
56: Excluding 3 bonded neighbours molecule type 'OCT'
56:
56: turning all bonds into constraints...
56:
56: Excluding 1 bonded neighbours molecule type 'NA'
56:
56: turning all bonds into constraints...
56:
56: Excluding 1 bonded neighbours molecule type 'CL'
56:
56: turning all bonds into constraints...
56:
56: Excluding 3 bonded neighbours molecule type 'Protein'
56:
56: Excluding 3 bonded neighbours molecule type 'OCT'
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning all bonds into constraints...
56:
56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
56:
56: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
56:
56: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
56:
56: Note that mdrun will redetermine rlist based on the actual pair-list setup
56:
56: This run will generate roughly 1 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 2.763 1.382 200.0
56: (ns/day) (hour/ns)
56: Performance: 0.938 25.589
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
56:
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: SWAP: Setting pointers for checkpoint writing
56: SWAP: Copying channel fluxes from checkpoint file data
56: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
56: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
56: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
56: starting mdrun 'Channel_coco in octane membrane'
56: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 2.579 1.290 200.0
56: (ns/day) (hour/ns)
56: Performance: 1.005 23.887
56: [ OK ] CompelTest.SwapCanRun (5394 ms)
56: [----------] 1 test from CompelTest (5395 ms total)
56:
56: [----------] 6 tests from BondedInteractionsTest
56: No protocol specified
56: [ RUN ] BondedInteractionsTest.NormalBondWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 2 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.001 0.001 183.4
56: (ns/day) (hour/ns)
56: Performance: 134.617 0.178
56: Setting the LD random seed to -1351781697
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalBondWorks (16 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 2 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.001 0.001 184.6
56: (ns/day) (hour/ns)
56: Performance: 130.637 0.184
56: Setting the LD random seed to 2130672622
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedBondWorks (19 ms)
56: [ RUN ] BondedInteractionsTest.NormalAngleWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.001 0.001 183.6
56: (ns/day) (hour/ns)
56: Performance: 131.015 0.183
56: Setting the LD random seed to -71995941
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalAngleWorks (17 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.001 0.001 183.0
56: (ns/day) (hour/ns)
56: Performance: 132.549 0.181
56: Setting the LD random seed to -9503763
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (18 ms)
56: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.001 0.001 183.7
56: (ns/day) (hour/ns)
56: Performance: 132.114 0.182
56: Setting the LD random seed to -18022532
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.NormalDihedralWorks (16 ms)
56: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
56: For a correct single-point energy evaluation with nsteps = 0, use
56: continuation = yes to avoid constraining the input coordinates.
56:
56:
56: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
56: In moleculetype 'butane' 4 atoms are not bound by a potential or
56: constraint to any other atom in the same moleculetype. Although
56: technically this might not cause issues in a simulation, this often means
56: that the user forgot to add a bond/potential/constraint or put multiple
56: molecules in the same moleculetype definition by mistake. Run with -v to
56: get information for each atom.
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: There were 3 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
56:
56: Reading frames from gro file 'A single butane', 4 atoms.
56:
Reading frame 0 time 0.000
Last frame 0 time 0.000
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.001 0.001 183.6
56: (ns/day) (hour/ns)
56: Performance: 130.684 0.184
56: Setting the LD random seed to -1085671961
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'butane'
56:
56: This run will generate roughly 0 Mb of data
56: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (20 ms)
56: [----------] 6 tests from BondedInteractionsTest (106 ms total)
56:
56: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest
56: No protocol specified
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0
56: Number of degrees of freedom in T-Coupling group rest is 10.00
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'Dipoles'
56: 20 steps, 0.1 ps.
56: Setting the LD random seed to 211130218
56:
56: Generated 1 of the 1 non-bonded parameter combinations
56:
56: Excluding 1 bonded neighbours molecule type 'Dipole'
56:
56: Searching the wall atom type(s)
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200
56:
56: Estimate for the relative computational load of the PME mesh part: 1.00
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.426 0.213 199.8
56: (ns/day) (hour/ns)
56: Performance: 21.264 1.129
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision)
56:
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (282 ms)
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1
56: Test system 'epsilon-surface-constraint' cannot run with 1 ranks.
56: The supported numbers are > 1.
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms)
56: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2
56:
56: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: With epsilon_surface > 0 all molecules should be neutral.
56:
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: With epsilon_surface > 0 you can only use domain decomposition when there
56: are only small molecules with all bonds constrained (mdrun will check for
56: this).
56:
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56:
56: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: NVE simulation with an initial temperature of zero: will use a Verlet
56: buffer of 10%. Check your energy drift!
56:
56:
56: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 4 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'Dipoles'
56: 20 steps, 0.1 ps.
56: Setting the LD random seed to 1916771030
56:
56: Generated 1 of the 1 non-bonded parameter combinations
56:
56: Excluding 1 bonded neighbours molecule type 'Dipole'
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200
56:
56: Estimate for the relative computational load of the PME mesh part: 1.00
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.394 0.197 199.8
56: (ns/day) (hour/ns)
56: Performance: 23.035 1.042
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Last energy frame read 5 time 0.050
56: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (225 ms)
56: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (507 ms total)
56:
56: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest
56: No protocol specified
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -1192953091
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.370 0.185 199.8
56: (ns/day) (hour/ns)
56: Performance: 2.335 10.280
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -44190393
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.336 0.168 199.7
56: (ns/day) (hour/ns)
56: Performance: 2.572 9.332
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (479 ms)
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to 771095351
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.358 0.179 199.8
56: (ns/day) (hour/ns)
56: Performance: 2.411 9.955
56: Generating 1-4 interactions: fudge = 0.5
56:
56: NOTE 1 [file ala.top, line 256]:
56: For energy conservation with LINCS, lincs_iter should be 2 or larger.
56:
56:
56: Number of degrees of freedom in T-Coupling group rest is 54.00
56:
56: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]:
56: The optimal PME mesh load for parallel simulations is below 0.5
56: and for highly parallel simulations between 0.25 and 0.33,
56: for higher performance, increase the cut-off and the PME grid spacing.
56:
56:
56:
56: There were 2 notes
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56:
56: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
56: starting mdrun 'UNNAMED in water'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -25703081
56:
56: Generated 2211 of the 2211 non-bonded parameter combinations
56:
56: Generated 2211 of the 2211 1-4 parameter combinations
56:
56: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
56:
56: turning H bonds into constraints...
56: Calculating fourier grid dimensions for X Y Z
56: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104
56:
56: Estimate for the relative computational load of the PME mesh part: 0.93
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.386 0.193 199.8
56: (ns/day) (hour/ns)
56: Performance: 2.237 10.727
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (491 ms)
56: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (970 ms total)
56:
56: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest
56: No protocol specified
56: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0
56: Generating 1-4 interactions: fudge = 0.5
56: Pull group 1 'FirstWaterMolecule' has 3 atoms
56: Pull group 2 'SecondWaterMolecule' has 3 atoms
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56: Pull group natoms pbc atom distance at start reference at t=0
56: 1 3 2
56: 2 3 5 1.112 nm 1.000 nm
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'spc2'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -536886300
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Generated 3 of the 3 1-4 parameter combinations
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.641 0.321 199.9
56: (ns/day) (hour/ns)
56: Performance: 1.347 17.813
56: Generating 1-4 interactions: fudge = 0.5
56: Pull group 1 'FirstWaterMolecule' has 3 atoms
56: Pull group 2 'SecondWaterMolecule' has 3 atoms
56: Number of degrees of freedom in T-Coupling group rest is 9.00
56: Pull group natoms pbc atom distance at start reference at t=0
56: 1 3 2
56: 2 3 5 1.112 nm 1.000 nm
56: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
56: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
56: Can not increase nstlist because an NVE ensemble is used
56: Using 1 MPI thread
56: Using 2 OpenMP threads
56:
56:
56: NOTE: The number of threads is not equal to the number of (logical) cores
56: and the -pin option is set to auto: will not pin threads to cores.
56: This can lead to significant performance degradation.
56: Consider using -pin on (and -pinoffset in case you run multiple jobs).
56:
56: WARNING: Using the slow plain C kernels. This should
56: not happen during routine usage on supported platforms.
56: starting mdrun 'spc2'
56: 4 steps, 0.0 ps.
56: Setting the LD random seed to -551633418
56:
56: Generated 3 of the 3 non-bonded parameter combinations
56:
56: Generated 3 of the 3 1-4 parameter combinations
56:
56: Excluding 2 bonded neighbours molecule type 'SOL'
56:
56: turning H bonds into constraints...
56:
56: This run will generate roughly 0 Mb of data
56:
56: Writing final coordinates.
56:
56: Core t (s) Wall t (s) (%)
56: Time: 0.522 0.261 199.9
56: (ns/day) (hour/ns)
56: Performance: 1.655 14.498
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004
56:
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
56: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
56:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Last energy frame read 1 time 0.004
Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (616 ms)
56: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (616 ms total)
56:
56: [----------] Global test environment tear-down
56: [==========] 14 tests from 6 test cases ran. (8423 ms total)
56: [ PASSED ] 14 tests.
56/65 Test #56: MdrunTests ............................ Passed 8.45 sec
test 57
Start 57: MdrunPmeTests
57: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-pme-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunPmeTests.xml"
57: Test timeout computed to be: 600
57: [==========] Running 3 tests from 1 test case.
57: [----------] Global test environment set-up.
57: [----------] 3 tests from PmeTest
57: No protocol specified
57: [ RUN ] PmeTest.ReproducesEnergies
57: Number of degrees of freedom in T-Coupling group rest is 12.00
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
57: NVE simulation: will use the initial temperature of 1046.791 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 2 notes
57: No protocol specified
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57: Setting the LD random seed to 670236268
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.497 0.249 199.9
57: (ns/day) (hour/ns)
57: Performance: 7.297 3.289
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.445 0.223 199.9
57: (ns/day) (hour/ns)
57: Performance: 8.154 2.943
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57:
57: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
57: starting mdrun 'spc-and-methanol'
57: 20 steps, 0.0 ps.
57:
57: Writing final coordinates.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.406 0.203 199.9
57: (ns/day) (hour/ns)
57: Performance: 8.933 2.687
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (755 ms)
57: [ RUN ] PmeTest.ScalesTheBox
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: For a correct single-point energy evaluation with nsteps = 0, use
57: continuation = yes to avoid constraining the input coordinates.
57:
57: Number of degrees of freedom in T-Coupling group rest is 12.00
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: NVE simulation: will use the initial temperature of 1046.791 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 3 notes
57: No protocol specified
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 0 steps, 0.0 ps.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.006 0.003 189.7
57: (ns/day) (hour/ns)
57: Performance: 26.541 0.904
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -182520968
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57: [ OK ] PmeTest.ScalesTheBox (52 ms)
57: [ RUN ] PmeTest.ScalesTheBoxWithWalls
57:
57: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: For a correct single-point energy evaluation with nsteps = 0, use
57: continuation = yes to avoid constraining the input coordinates.
57:
57: Number of degrees of freedom in T-Coupling group rest is 13.00
57:
57: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: NVE simulation: will use the initial temperature of 966.268 K for
57: determining the Verlet buffer size
57:
57:
57: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
57: The optimal PME mesh load for parallel simulations is below 0.5
57: and for highly parallel simulations between 0.25 and 0.33,
57: for higher performance, increase the cut-off and the PME grid spacing.
57:
57:
57:
57: There were 3 notes
57: No protocol specified
57: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
57: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
57: Can not increase nstlist because an NVE ensemble is used
57: Using 1 MPI thread
57: Using 2 OpenMP threads
57:
57:
57: NOTE: The number of threads is not equal to the number of (logical) cores
57: and the -pin option is set to auto: will not pin threads to cores.
57: This can lead to significant performance degradation.
57: Consider using -pin on (and -pinoffset in case you run multiple jobs).
57:
57: WARNING: Using the slow plain C kernels. This should
57: not happen during routine usage on supported platforms.
57: starting mdrun 'spc-and-methanol'
57: 0 steps, 0.0 ps.
57:
57: Core t (s) Wall t (s) (%)
57: Time: 0.029 0.015 197.3
57: (ns/day) (hour/ns)
57: Performance: 5.951 4.033
57: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
57:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1285556259
57:
57: Generated 8 of the 10 non-bonded parameter combinations
57:
57: Excluding 2 bonded neighbours molecule type 'Methanol'
57:
57: Excluding 2 bonded neighbours molecule type 'SOL'
57:
57: Searching the wall atom type(s)
57:
57: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
57:
57: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
57:
57: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
57:
57: Note that mdrun will redetermine rlist based on the actual pair-list setup
57: Calculating fourier grid dimensions for X Y Z
57: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
57:
57: Estimate for the relative computational load of the PME mesh part: 1.00
57:
57: This run will generate roughly 0 Mb of data
57: [ OK ] PmeTest.ScalesTheBoxWithWalls (97 ms)
57: [----------] 3 tests from PmeTest (904 ms total)
57:
57: [----------] Global test environment tear-down
57: [==========] 3 tests from 1 test case ran. (920 ms total)
57: [ PASSED ] 3 tests.
57/65 Test #57: MdrunPmeTests ......................... Passed 0.95 sec
test 58
Start 58: MdrunNonIntegratorTests
58: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml"
58: Test timeout computed to be: 600
58: [==========] Running 65 tests from 7 test cases.
58: [----------] Global test environment set-up.
58: [----------] 1 test from NonbondedBenchTest
58: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
58: System size: 3000 atoms
58: Cut-off radius: 1 nm
58: Number of threads: 1
58: Number of iterations: 1
58: Compute energies: no
58: Ewald excl. corr.: analytical
58:
58: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
58: total useful
58: Ewald all geom. no 0.000 0.0000 inf inf
58: [ OK ] NonbondedBenchTest.BasicEndToEndTest (304 ms)
58: [----------] 1 test from NonbondedBenchTest (304 ms total)
58:
58: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
58: No protocol specified
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -4.79910463671070e+01
58: Maximum force = 1.86297359432219e+02 on atom 13
58: Norm of force = 8.77219865482161e+01
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (2395 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 3.02331e+02 on atom 3
58: F-Norm = 1.18024e+02
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -5.58622538633290e+01
58: Maximum force = 4.27274822366527e+02 on atom 13
58: Norm of force = 1.84530029253829e+02
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2447 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 22.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 3.19376899751521e+02
58: Maximum force = 9.99884921009767e+03 on atom 9
58: Norm of force = 4.61669565054298e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: turning H bonds into constraints...
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (394 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58:
58: NOTE 3 [file glycine_vacuo.top, line 12]:
58: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
58:
58: Number of degrees of freedom in T-Coupling group System is 22.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 2.41575e+04 on atom 10
58: F-Norm = 1.18451e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 1.51743018140925e+02
58: Maximum force = 7.42089573409111e+03 on atom 9
58: Norm of force = 3.56929298615739e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: turning H bonds into constraints...
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (393 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -1.56984193848276e+02
58: Maximum force = 4.56923624626296e+02 on atom 17
58: Norm of force = 1.83258377168331e+02
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (51 ms)
58: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58:
58: NOTE 4 [file unknown]:
58: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 1.06800e+03 on atom 28
58: F-Norm = 4.26922e+02
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = -1.69410778678185e+02
58: Maximum force = 2.18225948473957e+02 on atom 17
58: Norm of force = 7.92068036537697e+01
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (52 ms)
58: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (5732 ms total)
58:
58: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
58: No protocol specified
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents converged to Fmax < 10 in 1 steps
58: Potential Energy = -9.74257075835450e-01
58: Maximum force = 4.01322929015108e+00 on atom 1
58: Norm of force = 1.63839399694368e+00
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (17 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 4.01323e+00 on atom 1
58: F-Norm = 1.63839e+00
58:
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
58: Potential Energy = -9.90642313893957e-01
58: Maximum force = 2.57812909491105e+00 on atom 1
58: Norm of force = 1.05251679559258e+00
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (21 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58:
58: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
58: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58:
58: There was 1 warning
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Low-Memory BFGS Minimizer:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: Using 10 BFGS correction steps.
58:
58: F-max = 4.01323e+00 on atom 1
58: F-Norm = 1.63839e+00
58:
58:
58: writing lowest energy coordinates.
58:
58: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
58: Potential Energy = -9.90642313893957e-01
58: Maximum force = 2.57812909491105e+00 on atom 1
58: Norm of force = 1.05251679559258e+00
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (18 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Steepest Descents:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Steepest Descents did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 3.19395484891517e+02
58: Maximum force = 9.97041707197910e+03 on atom 9
58: Norm of force = 4.62274878665467e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (410 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Polak-Ribiere Conjugate Gradients:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: F-max = 2.41672e+04 on atom 10
58: F-Norm = 1.19357e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 1.56258793899479e+02
58: Maximum force = 7.50181017480397e+03 on atom 9
58: Norm of force = 3.61390332564874e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (411 ms)
58: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58:
58: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
58:
58: Generating 1-4 interactions: fudge = 1
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58:
58: There was 1 warning
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Low-Memory BFGS Minimizer:
58: Tolerance (Fmax) = 1.00000e+01
58: Number of steps = 4
58: Using 10 BFGS correction steps.
58:
58: F-max = 2.41672e+04 on atom 10
58: F-Norm = 1.19357e+04
58:
58:
58: Energy minimization reached the maximum number of steps before the forces
58: reached the requested precision Fmax < 10.
58:
58: writing lowest energy coordinates.
58:
58: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
58: Potential Energy = 5.61116097794203e+02
58: Maximum force = 1.26854826291223e+04 on atom 10
58: Norm of force = 6.06436286976271e+03
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Glycine'
58:
58: This run will generate roughly 0 Mb of data
58: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (454 ms)
58: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1331 ms total)
58:
58: [----------] 5 tests from NormalModesWorks/NormalModesTest
58: No protocol specified
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 15.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=6), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation '2 scaled waters'
58: 12 steps.
58:
58: Maximum force: 9.96989e-06
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.3-Raspbian-2021.3-2
58:
58: Diagonalizing to find vectors 7 through 18...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--18 to eigenvec.trr
58: Generated 3 of the 3 non-bonded parameter combinations
58:
58: Generated 3 of the 3 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: There are: 6 Atoms
58: Using begin = 7 and end = 18
58: Full matrix storage format, nrow=18, ncols=18
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (99 ms)
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 1
58:
58: NOTE 3 [file villin.top, line 2452]:
58: System has non-zero total charge: -2.000000
58: Total charge should normally be an integer. See
58: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
58: for discussion on how close it should be to an integer.
58:
58:
58:
58: Number of degrees of freedom in T-Coupling group System is 765.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=256), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN'
58: 512 steps.
58:
58: Maximum force: 6.97568e-04
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.3-Raspbian-2021.3-2
58:
58: Diagonalizing to find vectors 7 through 50...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--50 to eigenvec.trr
58: Generated 20503 of the 20503 non-bonded parameter combinations
58:
58: Generated 17396 of the 20503 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
58:
58: This run will generate roughly 0 Mb of data
58: There are: 256 Atoms
58: Using begin = 7 and end = 50
58: Full matrix storage format, nrow=768, ncols=768
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (7716 ms)
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 15.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=6), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation 'flex spc dimer'
58: 12 steps.
58:
58: Maximum force: 3.36401e-04
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.3-Raspbian-2021.3-2
58:
58: Diagonalizing to find vectors 7 through 18...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--18 to eigenvec.trr
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: This run will generate roughly 0 Mb of data
58: There are: 6 Atoms
58: Using begin = 7 and end = 18
58: Full matrix storage format, nrow=18, ncols=18
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (2535 ms)
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
58: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
58: nstcomm to nstcalcenergy
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 6.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=3), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation '1 TIP5P'
58: 6 steps.
58:
58: Maximum force: 2.42882e-04
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.3-Raspbian-2021.3-2
58:
58: Diagonalizing to find vectors 7 through 9...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--9 to eigenvec.trr
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: This run will generate roughly 0 Mb of data
58: There are: 3 Atoms
58: There are: 2 VSites
58: Using begin = 7 and end = 9
58: Full matrix storage format, nrow=9, ncols=9
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (2412 ms)
58: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58: Number of degrees of freedom in T-Coupling group System is 15.00
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58:
58: Small system size (N=6), using full Hessian format.
58: Allocating Hessian memory...
58:
58: starting normal mode calculation 'sw dimer'
58: 12 steps.
58:
58: Maximum force: 1.07599e-03
58: The force is probably not small enough to ensure that you are at a minimum.
58: Be aware that negative eigenvalues may occur
58: when the resulting matrix is diagonalized.
58:
58:
58: Writing Hessian...
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Reading double precision matrix generated by GROMACS 2021.3-Raspbian-2021.3-2
58:
58: Diagonalizing to find vectors 7 through 18...
58: Writing eigenvalues...
58:
58: Writing average structure & eigenvectors 7--18 to eigenvec.trr
58: Generated 6 of the 10 non-bonded parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SW'
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: This run will generate roughly 0 Mb of data
58: There are: 6 Atoms
58: There are: 2 Shells
58: There are: 2 VSites
58:
58: NOTE: in the current version shell prediction during the crun is disabled
58:
58: Using begin = 7 and end = 18
58: Full matrix storage format, nrow=18, ncols=18
58: Writing eigenfrequencies - negative eigenvalues will be set to zero.
58: Cannot compute entropy when -first = 7
58: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (74 ms)
58: [----------] 5 tests from NormalModesWorks/NormalModesTest (12836 ms total)
58:
58: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
58: No protocol specified
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 68.810 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.350 0.175 199.9
58: (ns/day) (hour/ns)
58: Performance: 8.394 2.859
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
58:
58: trr version: GMX_trn_file (double precision)
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.003 0.002 193.8
58: (ns/day) (hour/ns)
58: Performance: 905.437 0.027
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (200 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 68.810 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.405 0.203 199.9
58: (ns/day) (hour/ns)
58: Performance: 7.253 3.309
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 193.8
58: (ns/day) (hour/ns)
58: Performance: 691.968 0.035
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (230 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.384 0.192 199.9
58: (ns/day) (hour/ns)
58: Performance: 7.651 3.137
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 193.6
58: (ns/day) (hour/ns)
58: Performance: 691.114 0.035
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (224 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Number of degrees of freedom in T-Coupling group System is 33.00
58:
58: There were 2 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Argon'
58: 16 steps, 0.0 ps.
58: Generated 1 of the 1 non-bonded parameter combinations
58:
58: Excluding 1 bonded neighbours molecule type 'Argon'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.334 0.167 199.9
58: (ns/day) (hour/ns)
58: Performance: 8.796 2.729
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 193.6
58: (ns/day) (hour/ns)
58: Performance: 693.292 0.035
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (199 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: NVE simulation: will use the initial temperature of 398.997 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.471 0.236 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.232 3.851
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 193.7
58: (ns/day) (hour/ns)
58: Performance: 645.494 0.037
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (2668 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: NVE simulation: will use the initial temperature of 398.997 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.480 0.240 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.123 3.919
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.002 193.9
58: (ns/day) (hour/ns)
58: Performance: 631.273 0.038
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (2667 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.462 0.231 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.354 3.777
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.004 0.002 194.0
58: (ns/day) (hour/ns)
58: Performance: 635.834 0.038
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (2658 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 27.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'spc2'
58: 16 steps, 0.0 ps.
58: Generated 330891 of the 330891 non-bonded parameter combinations
58:
58: Generated 330891 of the 330891 1-4 parameter combinations
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.419 0.210 199.9
58: (ns/day) (hour/ns)
58: Performance: 7.008 3.425
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 194.0
58: (ns/day) (hour/ns)
58: Performance: 587.171 0.041
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (2641 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: NVE simulation: will use the initial temperature of 456.887 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 6 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.406 0.203 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.227 3.321
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.003 195.1
58: (ns/day) (hour/ns)
58: Performance: 426.457 0.056
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (280 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: NVE simulation: will use the initial temperature of 456.887 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 6 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.396 0.198 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.413 3.238
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.004 195.1
58: (ns/day) (hour/ns)
58: Performance: 419.117 0.057
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (274 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.566 0.283 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.185 4.629
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.004 195.0
58: (ns/day) (hour/ns)
58: Performance: 418.348 0.057
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (405 ms)
58: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58:
58: NOTE 3 [file unknown]:
58: You are using constraints on all bonds, whereas the forcefield has been
58: parametrized only with constraints involving hydrogen atoms. We suggest
58: using constraints = h-bonds instead, this will also improve performance.
58:
58: Number of degrees of freedom in T-Coupling group System is 23.00
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: There are 9 non-linear virtual site constructions. Their contribution to
58: the energy error is approximated. In most cases this does not affect the
58: error significantly.
58:
58:
58: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 5 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'Alanine dipeptide in vacuo'
58: 16 steps, 0.0 ps.
58: Generated 2145 of the 2145 non-bonded parameter combinations
58:
58: Generated 2145 of the 2145 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
58:
58: turning all bonds into constraints...
58:
58: Cleaning up constraints and constant bonded interactions with virtual sites
58:
58: Removed 18 Angles with virtual sites, 21 left
58:
58: Removed 10 Proper Dih.s with virtual sites, 44 left
58:
58: Converted 15 Constraints with virtual sites to connections, 7 left
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.401 0.201 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.314 3.281
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.007 0.003 195.1
58: (ns/day) (hour/ns)
58: Performance: 421.814 0.057
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (307 ms)
58: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (12757 ms total)
58:
58: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
58: No protocol specified
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.500 0.250 199.8
58: (ns/day) (hour/ns)
58: Performance: 5.870 4.089
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 188.7
58: (ns/day) (hour/ns)
58: Performance: 357.405 0.067
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (334 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.596 0.298 199.8
58: (ns/day) (hour/ns)
58: Performance: 4.927 4.871
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 187.5
58: (ns/day) (hour/ns)
58: Performance: 518.656 0.046
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (375 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.471 0.236 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.227 3.854
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 189.1
58: (ns/day) (hour/ns)
58: Performance: 362.217 0.066
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (303 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.469 0.235 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.252 3.839
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 188.9
58: (ns/day) (hour/ns)
58: Performance: 367.336 0.065
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (319 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.562 0.281 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.224 4.594
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 184.3
58: (ns/day) (hour/ns)
58: Performance: 509.098 0.047
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (357 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.440 0.220 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.670 3.598
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 188.9
58: (ns/day) (hour/ns)
58: Performance: 363.414 0.066
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (299 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.496 0.248 199.8
58: (ns/day) (hour/ns)
58: Performance: 5.921 4.053
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 188.7
58: (ns/day) (hour/ns)
58: Performance: 365.354 0.066
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (332 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.447 0.224 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.568 3.654
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 188.2
58: (ns/day) (hour/ns)
58: Performance: 498.511 0.048
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (302 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.488 0.244 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.008 3.994
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 189.2
58: (ns/day) (hour/ns)
58: Performance: 358.863 0.067
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (313 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.578 0.289 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.077 4.728
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 182.7
58: (ns/day) (hour/ns)
58: Performance: 504.718 0.048
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (365 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.393 0.197 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.467 3.214
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 187.7
58: (ns/day) (hour/ns)
58: Performance: 517.349 0.046
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (266 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.662 0.331 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.434 5.413
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 188.8
58: (ns/day) (hour/ns)
58: Performance: 354.975 0.068
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (399 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.496 0.248 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.920 4.054
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 188.8
58: (ns/day) (hour/ns)
58: Performance: 364.748 0.066
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (332 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.530 0.265 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.542 4.330
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 189.1
58: (ns/day) (hour/ns)
58: Performance: 356.743 0.067
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (349 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.630 0.315 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.664 5.146
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 189.0
58: (ns/day) (hour/ns)
58: Performance: 357.509 0.067
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (399 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.479 0.240 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.131 3.915
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 189.1
58: (ns/day) (hour/ns)
58: Performance: 366.222 0.066
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (324 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.464 0.232 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.326 3.794
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 189.2
58: (ns/day) (hour/ns)
58: Performance: 355.960 0.067
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (316 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.712 0.356 200.0
58: (ns/day) (hour/ns)
58: Performance: 4.125 5.818
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 187.7
58: (ns/day) (hour/ns)
58: Performance: 517.697 0.046
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (431 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.499 0.250 199.9
58: (ns/day) (hour/ns)
58: Performance: 5.885 4.078
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 188.9
58: (ns/day) (hour/ns)
58: Performance: 367.577 0.065
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (324 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.463 0.232 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.342 3.784
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 184.1
58: (ns/day) (hour/ns)
58: Performance: 500.170 0.048
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (307 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.712 0.356 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.125 5.819
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 187.7
58: (ns/day) (hour/ns)
58: Performance: 515.229 0.047
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (417 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: NVE simulation: will use the initial temperature of 293.480 K for
58: determining the Verlet buffer size
58:
58:
58: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 4 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.475 0.238 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.180 3.883
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 188.9
58: (ns/day) (hour/ns)
58: Performance: 367.819 0.065
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (306 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.693 0.347 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.237 5.664
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 187.9
58: (ns/day) (hour/ns)
58: Performance: 510.575 0.047
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (454 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.482 0.241 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.089 3.941
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 189.0
58: (ns/day) (hour/ns)
58: Performance: 358.737 0.067
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (360 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.594 0.297 199.8
58: (ns/day) (hour/ns)
58: Performance: 4.943 4.855
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 184.4
58: (ns/day) (hour/ns)
58: Performance: 509.645 0.047
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (403 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.401 0.201 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.312 3.282
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 187.8
58: (ns/day) (hour/ns)
58: Performance: 514.584 0.047
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (289 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.448 0.224 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.554 3.662
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 188.0
58: (ns/day) (hour/ns)
58: Performance: 515.358 0.047
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (312 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.605 0.303 199.9
58: (ns/day) (hour/ns)
58: Performance: 4.849 4.949
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 187.9
58: (ns/day) (hour/ns)
58: Performance: 512.998 0.047
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (386 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.448 0.224 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.549 3.665
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.005 0.003 187.9
58: (ns/day) (hour/ns)
58: Performance: 504.099 0.048
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (307 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.447 0.224 199.8
58: (ns/day) (hour/ns)
58: Performance: 6.567 3.655
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 183.5
58: (ns/day) (hour/ns)
58: Performance: 470.706 0.051
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (308 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.399 0.200 199.8
58: (ns/day) (hour/ns)
58: Performance: 7.360 3.261
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.008 0.004 189.3
58: (ns/day) (hour/ns)
58: Performance: 339.090 0.071
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (296 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.475 0.238 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.178 3.885
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 188.2
58: (ns/day) (hour/ns)
58: Performance: 486.311 0.049
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (342 ms)
58: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: Setting nstcalcenergy (100) equal to nstenergy (4)
58:
58: Generating 1-4 interactions: fudge = 0.5
58: Number of degrees of freedom in T-Coupling group System is 79.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
58: You are using a plain Coulomb cut-off, which might produce artifacts.
58: You might want to consider using PME electrostatics.
58:
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun '30 system in water'
58: 16 steps, 0.0 ps.
58: Generated 2485 of the 2485 non-bonded parameter combinations
58:
58: Generated 2485 of the 2485 1-4 parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'nonanol'
58:
58: turning H bonds into constraints...
58:
58: Excluding 2 bonded neighbours molecule type 'SOL'
58:
58: turning H bonds into constraints...
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.472 0.236 199.9
58: (ns/day) (hour/ns)
58: Performance: 6.218 3.860
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
58:
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
58:
58:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.006 0.003 188.3
58: (ns/day) (hour/ns)
58: Performance: 488.355 0.049
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
58:
58: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (324 ms)
58: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (11253 ms total)
58:
58: [----------] 2 tests from Angles1/SimpleMdrunTest
58: No protocol specified
58: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file angles1.top, line 72]:
58: In moleculetype 'butane' 4 atoms are not bound by a potential or
58: constraint to any other atom in the same moleculetype. Although
58: technically this might not cause issues in a simulation, this often means
58: that the user forgot to add a bond/potential/constraint or put multiple
58: molecules in the same moleculetype definition by mistake. Run with -v to
58: get information for each atom.
58:
58: Number of degrees of freedom in T-Coupling group System is 9.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
58: NVE simulation: will use the initial temperature of 238.919 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'This_incredible_box_of_butane'
58: 50 steps, 0.1 ps.
58: Generated 3 of the 3 non-bonded parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'butane'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.406 0.203 199.9
58: (ns/day) (hour/ns)
58: Performance: 21.675 1.107
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
58: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (244 ms)
58: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1
58:
58: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
58: that with the Verlet scheme, nstlist has no effect on the accuracy of
58: your simulation.
58:
58:
58: NOTE 2 [file angles1.top, line 72]:
58: In moleculetype 'butane' 4 atoms are not bound by a potential or
58: constraint to any other atom in the same moleculetype. Although
58: technically this might not cause issues in a simulation, this often means
58: that the user forgot to add a bond/potential/constraint or put multiple
58: molecules in the same moleculetype definition by mistake. Run with -v to
58: get information for each atom.
58:
58: Number of degrees of freedom in T-Coupling group System is 9.00
58:
58: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
58: NVE simulation: will use the initial temperature of 238.919 K for
58: determining the Verlet buffer size
58:
58:
58: There were 3 notes
58: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
58: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
58: Can not increase nstlist because an NVE ensemble is used
58: Using 1 MPI thread
58: Using 2 OpenMP threads
58:
58:
58: NOTE: The number of threads is not equal to the number of (logical) cores
58: and the -pin option is set to auto: will not pin threads to cores.
58: This can lead to significant performance degradation.
58: Consider using -pin on (and -pinoffset in case you run multiple jobs).
58:
58: WARNING: Using the slow plain C kernels. This should
58: not happen during routine usage on supported platforms.
58: starting mdrun 'This_incredible_box_of_butane'
58: 50 steps, 0.1 ps.
58: Generated 3 of the 3 non-bonded parameter combinations
58:
58: Excluding 3 bonded neighbours molecule type 'butane'
58:
58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
58:
58: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
58:
58: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
58:
58: Note that mdrun will redetermine rlist based on the actual pair-list setup
58:
58: This run will generate roughly 0 Mb of data
58:
58: Writing final coordinates.
58:
58: Core t (s) Wall t (s) (%)
58: Time: 0.655 0.328 200.0
58: (ns/day) (hour/ns)
58: Performance: 13.445 1.785
58: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file
58:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
58: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (347 ms)
58: [----------] 2 tests from Angles1/SimpleMdrunTest (592 ms total)
58:
58: [----------] Global test environment tear-down
58: [==========] 65 tests from 7 test cases ran. (45011 ms total)
58: [ PASSED ] 65 tests.
58/65 Test #58: MdrunNonIntegratorTests ............... Passed 45.08 sec
test 59
Start 59: MdrunTpiTests
59: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml"
59: Test timeout computed to be: 600
59: [==========] Running 2 tests from 1 test case.
59: [----------] Global test environment set-up.
59: [----------] 2 tests from Simple/TpiTest
59: No protocol specified
59: [ RUN ] Simple/TpiTest.ReproducesOutput/0
59: Ignoring obsolete mdp entry 'ns_type'
59: Generating 1-4 interactions: fudge = 0.5
59: Number of degrees of freedom in T-Coupling group System is 1308.00
59: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
59: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
59: TPI is not implemented for GPUs.
59:
59: Using 1 MPI thread
59: Using 1 OpenMP thread
59:
59:
59: NOTE: Thread affinity was not set.
59:
59: WARNING: Using the slow plain C kernels. This should
59: not happen during routine usage on supported platforms.
59: Reading frames from gro file '216 water molecules', 648 atoms.
59:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
59:
Last frame 0 time 0.000
59: Generated 331705 of the 331705 non-bonded parameter combinations
59:
59: Generated 331705 of the 331705 1-4 parameter combinations
59:
59: Excluding 2 bonded neighbours molecule type 'SOL'
59:
59: Excluding 3 bonded neighbours molecule type 'methane'
59: Analysing residue names:
59: There are: 216 Water residues
59: There are: 1 Other residues
59: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
59:
59: This run will generate roughly 0 Mb of data
59: [ OK ] Simple/TpiTest.ReproducesOutput/0 (2474 ms)
59: [ RUN ] Simple/TpiTest.ReproducesOutput/1
59: Ignoring obsolete mdp entry 'ns_type'
59: Generating 1-4 interactions: fudge = 0.5
59: Number of degrees of freedom in T-Coupling group System is 1308.00
59: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
59: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
59: TPI is not implemented for GPUs.
59:
59: Using 1 MPI thread
59: Using 1 OpenMP thread
59:
59:
59: NOTE: Thread affinity was not set.
59:
59: WARNING: Using the slow plain C kernels. This should
59: not happen during routine usage on supported platforms.
59: Reading frames from gro file '216 water molecules', 648 atoms.
59:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
59:
Last frame 0 time 0.000
59: Generated 331705 of the 331705 non-bonded parameter combinations
59:
59: Generated 331705 of the 331705 1-4 parameter combinations
59:
59: Excluding 2 bonded neighbours molecule type 'SOL'
59:
59: Excluding 3 bonded neighbours molecule type 'methane'
59: Analysing residue names:
59: There are: 216 Water residues
59: There are: 1 Other residues
59: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
59:
59: This run will generate roughly 0 Mb of data
59: [ OK ] Simple/TpiTest.ReproducesOutput/1 (2519 ms)
59: [----------] 2 tests from Simple/TpiTest (4993 ms total)
59:
59: [----------] Global test environment tear-down
59: [==========] 2 tests from 1 test case ran. (5015 ms total)
59: [ PASSED ] 2 tests.
59/65 Test #59: MdrunTpiTests ......................... Passed 5.05 sec
test 60
Start 60: MdrunMpiTests
60: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml"
60: Test timeout computed to be: 600
60: [==========] Running 22 tests from 7 test cases.
60: [----------] Global test environment set-up.
60: [----------] 1 test from DomainDecompositionSpecialCasesTest
60: No protocol specified
60: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 9.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc2'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.002 0.001 259.5
60: (ns/day) (hour/ns)
60: Performance: 143.321 0.167
60: Setting the LD random seed to -550175877
60:
60: Generated 3 of the 3 non-bonded parameter combinations
60:
60: Generated 3 of the 3 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (21 ms)
60: [----------] 1 test from DomainDecompositionSpecialCasesTest (22 ms total)
60:
60: [----------] 4 tests from MimicTest
60: No protocol specified
60: [ RUN ] MimicTest.OneQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.479 0.650 381.5
60: (ns/day) (hour/ns)
60: Performance: 0.133 180.497
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -1225261473
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.OneQuantumMol (2048 ms)
60: [ RUN ] MimicTest.AllQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.419 0.635 381.1
60: (ns/day) (hour/ns)
60: Performance: 0.136 176.342
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 2129591479
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.AllQuantumMol (2030 ms)
60: [ RUN ] MimicTest.TwoQuantumMol
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 21.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: NVE simulation with an initial temperature of zero: will use a Verlet
60: buffer of 10%. Check your energy drift!
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
60:
60: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.499 0.655 381.7
60: (ns/day) (hour/ns)
60: Performance: 0.132 181.877
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -3146063
60:
60: Generated 10 of the 10 non-bonded parameter combinations
60:
60: Generated 10 of the 10 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.TwoQuantumMol (2058 ms)
60: [ RUN ] MimicTest.BondCuts
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group rest is 66.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: NVE simulation: will use the initial temperature of 300.368 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
60:
60: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
60:
Reading frame 0 time 0.000
Last frame 0 time 0.000
60:
60: Core t (s) Wall t (s) (%)
60: Time: 2.339 0.615 380.5
60: (ns/day) (hour/ns)
60: Performance: 0.141 170.784
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 1207418827
60:
60: Generated 2211 of the 2211 non-bonded parameter combinations
60:
60: Generated 2211 of the 2211 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MimicTest.BondCuts (1999 ms)
60: [----------] 4 tests from MimicTest (8140 ms total)
60:
60: [----------] 1 test from MultiSimTerminationTest
60: No protocol specified
60: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
60: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
60: [----------] 1 test from MultiSimTerminationTest (1 ms total)
60:
60: [----------] 1 test from ReplicaExchangeTerminationTest
60: No protocol specified
60: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
60: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
60: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
60:
60: [----------] 3 tests from PmeTest
60: No protocol specified
60: [ RUN ] PmeTest.ReproducesEnergies
60: Number of degrees of freedom in T-Coupling group rest is 12.00
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
60: NVE simulation: will use the initial temperature of 1046.791 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 2 notes
60: No protocol specified
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60: Setting the LD random seed to -315621397
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 5.271 1.360 387.6
60: (ns/day) (hour/ns)
60: Performance: 1.334 17.988
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 5.350 1.380 387.7
60: (ns/day) (hour/ns)
60: Performance: 1.315 18.253
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
60: starting mdrun 'spc-and-methanol'
60: 20 steps, 0.0 ps.
60:
60: Writing final coordinates.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 5.311 1.370 387.8
60: (ns/day) (hour/ns)
60: Performance: 1.325 18.118
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (6824 ms)
60: [ RUN ] PmeTest.ScalesTheBox
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Number of degrees of freedom in T-Coupling group rest is 12.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: NVE simulation: will use the initial temperature of 1046.791 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 3 notes
60: No protocol specified
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.222 0.095 234.4
60: (ns/day) (hour/ns)
60: Performance: 0.910 26.362
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -538445317
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] PmeTest.ScalesTheBox (1009 ms)
60: [ RUN ] PmeTest.ScalesTheBoxWithWalls
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: For a correct single-point energy evaluation with nsteps = 0, use
60: continuation = yes to avoid constraining the input coordinates.
60:
60: Number of degrees of freedom in T-Coupling group rest is 13.00
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: NVE simulation: will use the initial temperature of 966.268 K for
60: determining the Verlet buffer size
60:
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
60: The optimal PME mesh load for parallel simulations is below 0.5
60: and for highly parallel simulations between 0.25 and 0.33,
60: for higher performance, increase the cut-off and the PME grid spacing.
60:
60:
60:
60: There were 3 notes
60: No protocol specified
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Can not increase nstlist because an NVE ensemble is used
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60: Using 0 OpenMP thread per tMPI thread for PME
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60: starting mdrun 'spc-and-methanol'
60: 0 steps, 0.0 ps.
60:
60: Core t (s) Wall t (s) (%)
60: Time: 0.382 0.140 273.3
60: (ns/day) (hour/ns)
60: Performance: 0.618 38.859
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to 520084651
60:
60: Generated 8 of the 10 non-bonded parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'Methanol'
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: Searching the wall atom type(s)
60:
60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
60:
60: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
60:
60: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
60:
60: Note that mdrun will redetermine rlist based on the actual pair-list setup
60: Calculating fourier grid dimensions for X Y Z
60: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
60:
60: Estimate for the relative computational load of the PME mesh part: 1.00
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] PmeTest.ScalesTheBoxWithWalls (1021 ms)
60: [----------] 3 tests from PmeTest (8855 ms total)
60:
60: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
60: No protocol specified
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -4.79910463671071e+01
60: Maximum force = 1.86297359432220e+02 on atom 13
60: Norm of force = 8.77219865482161e+01
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
60:
60: Generated 330891 of the 330891 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (5298 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 3.02331e+02 on atom 3
60: F-Norm = 1.18024e+02
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -5.58622538633291e+01
60: Maximum force = 4.27274822366526e+02 on atom 13
60: Norm of force = 1.84530029253829e+02
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations
60:
60: Generated 330891 of the 330891 1-4 parameter combinations
60:
60: Excluding 2 bonded neighbours molecule type 'SOL'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (6946 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 22.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 3.19376899751521e+02
60: Maximum force = 9.99884921009767e+03 on atom 9
60: Norm of force = 4.61669565054298e+03
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: turning H bonds into constraints...
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (3431 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60:
60: NOTE 3 [file glycine_vacuo.top, line 12]:
60: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
60:
60: Number of degrees of freedom in T-Coupling group System is 22.00
60:
60: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 4 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 2.41575e+04 on atom 10
60: F-Norm = 1.18451e+04
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 1.51743018140926e+02
60: Maximum force = 7.42089573409112e+03 on atom 9
60: Norm of force = 3.56929298615739e+03
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: turning H bonds into constraints...
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (4925 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60:
60: NOTE 3 [file unknown]:
60: You are using constraints on all bonds, whereas the forcefield has been
60: parametrized only with constraints involving hydrogen atoms. We suggest
60: using constraints = h-bonds instead, this will also improve performance.
60:
60: Number of degrees of freedom in T-Coupling group System is 23.00
60:
60: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 4 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -1.56984193848276e+02
60: Maximum force = 4.56923624626296e+02 on atom 17
60: Norm of force = 1.83258377168331e+02
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations
60:
60: Generated 2145 of the 2145 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
60:
60: turning all bonds into constraints...
60:
60: Cleaning up constraints and constant bonded interactions with virtual sites
60:
60: Removed 18 Angles with virtual sites, 21 left
60:
60: Removed 10 Proper Dih.s with virtual sites, 44 left
60:
60: Converted 15 Constraints with virtual sites to connections, 7 left
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (4217 ms)
60: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 0.5
60:
60: NOTE 3 [file unknown]:
60: You are using constraints on all bonds, whereas the forcefield has been
60: parametrized only with constraints involving hydrogen atoms. We suggest
60: using constraints = h-bonds instead, this will also improve performance.
60:
60:
60: NOTE 4 [file unknown]:
60: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
60:
60: Number of degrees of freedom in T-Coupling group System is 23.00
60:
60: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 5 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 1.06800e+03 on atom 28
60: F-Norm = 4.26922e+02
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = -1.69410778678185e+02
60: Maximum force = 2.18225948474048e+02 on atom 17
60: Norm of force = 7.92068036537643e+01
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations
60:
60: Generated 2145 of the 2145 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
60:
60: turning all bonds into constraints...
60:
60: Cleaning up constraints and constant bonded interactions with virtual sites
60:
60: Removed 18 Angles with virtual sites, 21 left
60:
60: Removed 10 Proper Dih.s with virtual sites, 44 left
60:
60: Converted 15 Constraints with virtual sites to connections, 7 left
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (6205 ms)
60: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (31042 ms total)
60:
60: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
60: No protocol specified
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents converged to Fmax < 10 in 1 steps
60: Potential Energy = -9.74257075835450e-01
60: Maximum force = 4.01322929015108e+00 on atom 3
60: Norm of force = 1.63839399694368e+00
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (1643 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 4.01323e+00 on atom 3
60: F-Norm = 1.63839e+00
60:
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
60: Potential Energy = -9.90642313893957e-01
60: Maximum force = 2.57812909491105e+00 on atom 3
60: Norm of force = 1.05251679559258e+00
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (2078 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60:
60: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
60: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
60:
60: Number of degrees of freedom in T-Coupling group System is 33.00
60:
60: There were 2 notes
60:
60: There was 1 warning
60: Generated 1 of the 1 non-bonded parameter combinations
60:
60: Excluding 1 bonded neighbours molecule type 'Argon'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (10 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Steepest Descents:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Steepest Descents did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 3.19395484891518e+02
60: Maximum force = 9.97041707197910e+03 on atom 9
60: Norm of force = 4.62274878665467e+03
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (3058 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
60: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
60: Using 2 MPI threads
60:
60: Non-default thread affinity set, disabling internal thread affinity
60:
60: Using 2 OpenMP threads per tMPI thread
60:
60:
60: WARNING: Using the slow plain C kernels. This should
60: not happen during routine usage on supported platforms.
60:
60: Polak-Ribiere Conjugate Gradients:
60: Tolerance (Fmax) = 1.00000e+01
60: Number of steps = 4
60: F-max = 2.41672e+04 on atom 10
60: F-Norm = 1.19357e+04
60:
60:
60: Energy minimization reached the maximum number of steps before the forces
60: reached the requested precision Fmax < 10.
60:
60: writing lowest energy coordinates.
60:
60: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
60: Potential Energy = 1.56258793899479e+02
60: Maximum force = 7.50181017480397e+03 on atom 9
60: Norm of force = 3.61390332564874e+03
60: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
60:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (4486 ms)
60: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
60:
60: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
60: that with the Verlet scheme, nstlist has no effect on the accuracy of
60: your simulation.
60:
60:
60: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
60: nstcomm to nstcalcenergy
60:
60:
60: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
60:
60: Generating 1-4 interactions: fudge = 1
60: Number of degrees of freedom in T-Coupling group System is 27.00
60:
60: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
60: You are using a plain Coulomb cut-off, which might produce artifacts.
60: You might want to consider using PME electrostatics.
60:
60:
60:
60: There were 3 notes
60:
60: There was 1 warning
60: Generated 20503 of the 20503 non-bonded parameter combinations
60:
60: Generated 17396 of the 20503 1-4 parameter combinations
60:
60: Excluding 3 bonded neighbours molecule type 'Glycine'
60:
60: This run will generate roughly 0 Mb of data
60: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (389 ms)
60: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (11676 ms total)
60:
60: [----------] Global test environment tear-down
60: [==========] 22 tests from 7 test cases ran. (59888 ms total)
60: [ PASSED ] 22 tests.
60:
60: YOU HAVE 4 DISABLED TESTS
60:
60/65 Test #60: MdrunMpiTests ......................... Passed 59.93 sec
test 61
Start 61: MdrunMpiPmeTests
61: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiPmeTests.xml"
61: Test timeout computed to be: 600
61: [==========] Running 3 tests from 1 test case.
61: [----------] Global test environment set-up.
61: [----------] 3 tests from PmeTest
61: No protocol specified
61: [ RUN ] PmeTest.ReproducesEnergies
61: Number of degrees of freedom in T-Coupling group rest is 12.00
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
61: NVE simulation: will use the initial temperature of 1046.791 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 2 notes
61: No protocol specified
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61: Setting the LD random seed to -272646406
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.858 0.215 399.7
61: (ns/day) (hour/ns)
61: Performance: 8.450 2.840
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 5.229 1.350 387.3
61: (ns/day) (hour/ns)
61: Performance: 1.344 17.856
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61:
61: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
61: starting mdrun 'spc-and-methanol'
61: 20 steps, 0.0 ps.
61:
61: Writing final coordinates.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 5.254 1.355 387.8
61: (ns/day) (hour/ns)
61: Performance: 1.339 17.921
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (4738 ms)
61: [ RUN ] PmeTest.ScalesTheBox
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: For a correct single-point energy evaluation with nsteps = 0, use
61: continuation = yes to avoid constraining the input coordinates.
61:
61: Number of degrees of freedom in T-Coupling group rest is 12.00
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: NVE simulation: will use the initial temperature of 1046.791 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 3 notes
61: No protocol specified
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 0 steps, 0.0 ps.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.243 0.105 231.2
61: (ns/day) (hour/ns)
61: Performance: 0.824 29.135
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -538050567
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61: [ OK ] PmeTest.ScalesTheBox (1020 ms)
61: [ RUN ] PmeTest.ScalesTheBoxWithWalls
61:
61: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: For a correct single-point energy evaluation with nsteps = 0, use
61: continuation = yes to avoid constraining the input coordinates.
61:
61: Number of degrees of freedom in T-Coupling group rest is 13.00
61:
61: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: NVE simulation: will use the initial temperature of 966.268 K for
61: determining the Verlet buffer size
61:
61:
61: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
61: The optimal PME mesh load for parallel simulations is below 0.5
61: and for highly parallel simulations between 0.25 and 0.33,
61: for higher performance, increase the cut-off and the PME grid spacing.
61:
61:
61:
61: There were 3 notes
61: No protocol specified
61: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
61: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
61: Can not increase nstlist because an NVE ensemble is used
61: Using 2 MPI threads
61:
61: Non-default thread affinity set, disabling internal thread affinity
61:
61: Using 2 OpenMP threads per tMPI thread
61:
61:
61: WARNING: Using the slow plain C kernels. This should
61: not happen during routine usage on supported platforms.
61: starting mdrun 'spc-and-methanol'
61: 0 steps, 0.0 ps.
61:
61: Core t (s) Wall t (s) (%)
61: Time: 0.400 0.140 286.2
61: (ns/day) (hour/ns)
61: Performance: 0.618 38.860
61: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
61:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Setting the LD random seed to -280297474
61:
61: Generated 8 of the 10 non-bonded parameter combinations
61:
61: Excluding 2 bonded neighbours molecule type 'Methanol'
61:
61: Excluding 2 bonded neighbours molecule type 'SOL'
61:
61: Searching the wall atom type(s)
61:
61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
61:
61: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
61:
61: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
61:
61: Note that mdrun will redetermine rlist based on the actual pair-list setup
61: Calculating fourier grid dimensions for X Y Z
61: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
61:
61: Estimate for the relative computational load of the PME mesh part: 1.00
61:
61: This run will generate roughly 0 Mb of data
61: [ OK ] PmeTest.ScalesTheBoxWithWalls (1130 ms)
61: [----------] 3 tests from PmeTest (6888 ms total)
61:
61: [----------] Global test environment tear-down
61: [==========] 3 tests from 1 test case ran. (6911 ms total)
61: [ PASSED ] 3 tests.
61/65 Test #61: MdrunMpiPmeTests ...................... Passed 6.94 sec
test 62
Start 62: MdrunMpiCoordinationTestsOneRank
62: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
62: Test timeout computed to be: 1920
62: [==========] Running 39 tests from 3 test cases.
62: [----------] Global test environment set-up.
62: [----------] 1 test from BasicPropagators/PeriodicActionsTest
62: No protocol specified
62: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.222 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.607 3.633
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.184 0.184 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.963 3.014
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.201 3.333
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.179 0.179 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.190 2.930
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.288 0.288 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.096 4.710
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.196 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.491 3.204
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1354 ms)
62: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1354 ms total)
62:
62: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest
62: No protocol specified
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.183 0.184 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.002 2.999
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.173 0.173 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.472 2.833
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.199 0.200 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.358 3.262
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.202 0.202 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.262 3.305
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.286 0.286 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.129 4.679
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.161 0.161 99.9
62: (ns/day) (hour/ns)
62: Performance: 9.098 2.638
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1323 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.174 0.174 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.421 2.850
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.177 0.177 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.293 2.894
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.200 0.200 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.333 3.273
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.227 0.227 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.465 3.712
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.211 0.211 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.946 3.455
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.228 0.228 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.438 3.728
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1304 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.268 0.268 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.475 4.384
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.217 0.217 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.766 3.547
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.221 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.648 3.610
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.254 0.254 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.780 4.152
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.254 0.254 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.773 4.157
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.263 0.263 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.591 4.292
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1553 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.212 0.212 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.927 3.465
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.222 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.609 3.631
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.212 0.212 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.915 3.471
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.220 0.221 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.656 3.606
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.183 3.341
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.205 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.178 3.344
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1354 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.186 0.186 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.879 3.046
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.180 0.180 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.146 2.946
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.187 0.187 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.839 3.062
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.295 0.295 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.972 4.827
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.196 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.493 3.203
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.196 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.493 3.203
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1313 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.203 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.231 3.319
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.296 0.297 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.952 4.847
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.220 0.221 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.661 3.603
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.195 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.521 3.191
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.221 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.649 3.610
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.190 3.338
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1412 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.228 0.228 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.448 3.722
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.172 0.172 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.549 2.807
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.237 0.237 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.191 3.876
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.200 3.333
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.205 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.180 3.343
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.287 0.287 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.109 4.698
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1404 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.203 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.241 3.314
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.230 0.230 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.379 3.762
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.205 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.170 3.347
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.188 0.188 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.794 3.079
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.287 0.287 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.110 4.696
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.196 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.494 3.203
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1395 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.195 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.546 3.180
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.214 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.879 3.489
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.187 0.188 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.831 3.065
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.312 0.312 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.706 5.100
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.188 0.188 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.817 3.070
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.903 3.477
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1379 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.186 0.186 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.886 3.043
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.205 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.157 3.354
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.303 0.304 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.836 4.962
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.245 0.246 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.982 4.012
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.186 3.340
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62:
62: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
62: Using Berendsen pressure coupling invalidates the true ensemble for the
62: thermostat
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62:
62: There was 1 warning
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.221 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.646 3.611
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1438 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.294 0.294 100.0
62: (ns/day) (hour/ns)
62: Performance: 4.990 4.810
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.230 0.230 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.385 3.759
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.199 3.334
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.220 0.221 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.660 3.604
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.296 0.297 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.954 4.845
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.223 0.223 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.572 3.652
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1556 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.187 0.187 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.851 3.057
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.224 0.225 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.539 3.671
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.198 3.334
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.223 0.224 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.569 3.654
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.205 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.157 3.353
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
62: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.206 0.206 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.129 3.367
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1368 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.161 0.161 99.9
62: (ns/day) (hour/ns)
62: Performance: 9.100 2.637
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.271 0.272 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.408 4.438
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.194 3.336
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.171 0.171 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.595 2.792
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.163 0.164 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.977 2.673
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.202 0.202 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.270 3.301
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1246 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.237 0.237 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.203 3.869
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.350 0.350 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.196 5.720
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.223 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.593 3.640
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.230 0.230 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.380 3.762
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.881 3.488
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.289 0.289 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.076 4.728
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1670 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.193 0.194 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.590 3.162
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.884 3.486
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.214 0.215 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.843 3.507
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.331 0.331 99.8
62: (ns/day) (hour/ns)
62: Performance: 4.433 5.414
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.221 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.631 3.619
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.197 0.197 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.461 3.217
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (1482 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.219 0.220 100.0
62: (ns/day) (hour/ns)
62: Performance: 6.690 3.587
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.882 3.487
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.312 0.312 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.705 5.101
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.237 0.237 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.190 3.877
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.270 0.270 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.432 4.418
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.215 3.326
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1542 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.286 0.286 100.0
62: (ns/day) (hour/ns)
62: Performance: 5.136 4.673
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.240 0.240 100.0
62: (ns/day) (hour/ns)
62: Performance: 6.129 3.916
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 100.0
62: (ns/day) (hour/ns)
62: Performance: 6.904 3.476
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.196 100.0
62: (ns/day) (hour/ns)
62: Performance: 7.500 3.200
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.321 0.321 100.0
62: (ns/day) (hour/ns)
62: Performance: 4.578 5.243
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.206 0.206 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.133 3.365
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (1548 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.219 0.219 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.699 3.583
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.230 0.230 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.383 3.760
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.279 0.280 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.252 4.570
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.237 0.237 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.198 3.872
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.228 0.229 99.7
62: (ns/day) (hour/ns)
62: Performance: 6.421 3.738
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.206 0.206 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.128 3.367
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (1517 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.187 0.187 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.865 3.051
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.332 0.333 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.416 5.435
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.197 3.335
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.205 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.173 3.346
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.193 0.194 99.7
62: (ns/day) (hour/ns)
62: Performance: 7.579 3.167
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]:
62: NVE simulation: will use the initial temperature of 68.810 K for
62: determining the Verlet buffer size
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.324 0.324 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.528 5.301
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (1545 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.625 0.625 100.0
62: (ns/day) (hour/ns)
62: Performance: 2.349 10.218
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.227 0.227 100.0
62: (ns/day) (hour/ns)
62: Performance: 6.471 3.709
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.337 0.337 100.0
62: (ns/day) (hour/ns)
62: Performance: 4.359 5.506
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.885 3.486
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.232 0.232 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.324 3.795
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.197 0.197 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.451 3.221
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (1964 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.283 0.283 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.182 4.631
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.224 0.224 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.558 3.660
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.204 0.205 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.171 3.347
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.206 0.206 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.113 3.374
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.172 0.172 99.6
62: (ns/day) (hour/ns)
62: Performance: 8.522 2.816
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.281 0.281 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.223 4.595
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (1512 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.217 0.217 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.771 3.545
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.225 0.225 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.525 3.678
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.198 0.198 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.409 3.239
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.206 0.206 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.122 3.370
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.207 0.207 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.096 3.382
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.232 0.232 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.322 3.797
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (1429 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.278 0.279 100.0
62: (ns/day) (hour/ns)
62: Performance: 5.272 4.552
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.238 0.238 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.159 3.896
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.221 0.222 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.622 3.624
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.222 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.611 3.630
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.288 0.288 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.093 4.712
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.223 0.223 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.594 3.640
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (1583 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.203 0.204 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.210 3.329
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.216 0.217 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.778 3.541
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.280 0.280 99.8
62: (ns/day) (hour/ns)
62: Performance: 5.244 4.576
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.273 0.273 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.382 4.459
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.223 0.223 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.579 3.648
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.222 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.604 3.634
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (1562 ms)
62: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.261 0.262 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.616 4.274
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.209 0.209 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.028 3.415
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.222 0.222 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.605 3.633
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.206 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.138 3.362
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.200 0.200 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.343 3.268
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Number of degrees of freedom in T-Coupling group System is 33.00
62:
62: There were 2 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'Argon'
62: 16 steps, 0.0 ps.
62: Generated 1 of the 1 non-bonded parameter combinations
62:
62: Excluding 1 bonded neighbours molecule type 'Argon'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.313 0.314 99.9
62: (ns/day) (hour/ns)
62: Performance: 4.684 5.123
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file
62: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (1537 ms)
62: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (36936 ms total)
62:
62: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest
62: No protocol specified
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.179 0.180 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.181 2.934
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.236 0.236 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.218 3.860
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.192 99.8
62: (ns/day) (hour/ns)
62: Performance: 7.652 3.136
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.197 0.197 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.440 3.226
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.174 0.175 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.410 2.854
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.270 0.270 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.442 4.410
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (13188 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.234 0.234 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.272 3.827
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.291 0.291 99.9
62: (ns/day) (hour/ns)
62: Performance: 5.047 4.755
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.197 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.474 3.211
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.195 0.196 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.511 3.195
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.193 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.629 3.146
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.196 0.196 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.487 3.205
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (14423 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.255 0.255 100.0
62: (ns/day) (hour/ns)
62: Performance: 5.751 4.173
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.205 0.206 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.146 3.359
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.220 0.221 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.659 3.604
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.232 0.232 99.9
62: (ns/day) (hour/ns)
62: Performance: 6.324 3.795
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.213 0.213 99.8
62: (ns/day) (hour/ns)
62: Performance: 6.886 3.486
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: NVE simulation: will use the initial temperature of 398.997 K for
62: determining the Verlet buffer size
62:
62:
62: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 4 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Can not increase nstlist because an NVE ensemble is used
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.192 0.192 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.633 3.144
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
62: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (14885 ms)
62: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.208 0.208 99.9
62: (ns/day) (hour/ns)
62: Performance: 7.045 3.407
62:
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.176 0.176 99.9
62: (ns/day) (hour/ns)
62: Performance: 8.324 2.883
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: You are using a plain Coulomb cut-off, which might produce artifacts.
62: You might want to consider using PME electrostatics.
62:
62:
62:
62: There were 3 notes
62: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
62: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2021.3-Raspbian-2021.3-2 (double precision)
62: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
62:
62: Using 1 MPI thread
62: Using 1 OpenMP thread
62:
62:
62: NOTE: Thread affinity was not set.
62:
62: WARNING: Using the slow plain C kernels. This should
62: not happen during routine usage on supported platforms.
62: starting mdrun 'spc2'
62: 16 steps, 0.0 ps.
62: Generated 330891 of the 330891 non-bonded parameter combinations
62:
62: Generated 330891 of the 330891 1-4 parameter combinations
62:
62: Excluding 2 bonded neighbours molecule type 'SOL'
62:
62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
62:
62: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
62:
62: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
62:
62: Note that mdrun will redetermine rlist based on the actual pair-list setup
62:
62: This run will generate roughly 0 Mb of data
62:
62: Writing final coordinates.
62:
62: Core t (s) Wall t (s) (%)
62: Time: 0.172 0.172 99.8
62: (ns/day) (hour/ns)
62: Performance: 8.537 2.811
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
62: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
62:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
62: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
62: that with the Verlet scheme, nstlist has no effect on the accuracy of
62: your simulation.
62:
62:
62: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
62: Setting nstcalcenergy (100) equal to nstenergy (4)
62:
62: Generating 1-4 interactions: fudge = 0.5
62: Number of degrees of freedom in T-Coupling group System is 27.00
62:
62: NOTE 3 [file /<<PKGBUILDDIR>>